M5OD intermittent issues

[Caballero5.7]

Afternoon folks, new member here. I’ve been all over google trying to scrape together some knowledge but I’m coming up dry. I’ve been working on vehicles for about 20 years, but I’ve never had to troubleshoot a manual transmission. The problems I’m having are sporadic but have certain criteria they trigger in, and I’d appreciate any advice and experience from more experienced members. Sorry in advance for the essay!

I have a new to me ‘03 Level II with 195k on the clock. I fully expect things to be a bit worn out by this point. I have bled the clutch and changed the fluid with Amsoil Mercon V compliant ATF.

Issue #1:
1st, 2nd, and 3rd shifts are slow to engage, and won’t “fall” into gear until a second or two have passed of gently pushing toward the gear. I’m assuming this is synchro related, and I unfortunately believe I have the 3 piece synchros based off the year/engine. These are massively more expensive/uncommon than the two piece synchro design, and I assume they’re NOT interchangeable. I see rebuilt transmissions for sale on the internet for $1500, and judging by the fact that a 3 piece kit is $800 alone, I’m guessing that these are non HD models with the two piece design.

Issue #2:
When downshifting into first at speed, I’ve started hearing a “pssssh” like a blowoff valve, followed by the strong smell of ATF. This only happens going into first, and almost exclusively on downshifts, though it did happen the other day when I put it in first to pull away from a gas pump. I know the shift rail plugs disintegrate over time, and I haven’t checked them, but why does it sound pressurized if there are potentially big open holes there? Is there a breather tube that may be clogged? Why is it only first gear that does this?

Issue #3:
Sometimes when shifting into first, it simply won’t shift, as if there’s a blocker. Releasing the shifter and pushing it back towards first works 90% of the time. Makes red light takeoffs a bit stressful.

Issue #4:
Sometimes when you shift into first, the lever positively pops into gear, and about half a second later, the whole lever chatters for about a second, like two gears trying to mesh at speed, but I’m already in the gear??

Issue #5:
After starting the engine and ensuring the vehicle is in neutral, releasing the clutch quickly makes an “rrrrr” grinding noise for a split second after the clutch is fully released into neutral. This noise only recently stated happening, and only when the vehicle is first started. Could the rapid disengagement be pressuring the throwout or input bearing enough to make this noise? I can’t reliably recreate this except when I first start the truck.

 

[Curious Hound]

My first impression is that the clutch may not be fully disengaging. The next thing is that it sounds like the atf is wrong. As if something is not allowing the synchronizers to slide or grab as needed. Does it get any better after everything heats up from driving a while?

Does your manual call for Mercon V or Mercon IV?

 

[lowspeedpursuit]

I agree the clutch dragging was my first thought. Why were you bleeding it? If it wasn't fully disengaging in the first place, it's probably leaking.


Random thoughts on everything point-by-point:
There was another poster who just sourced a rebuilt HD like 2-3 weeks ago for $1300.

M5OD vents through the shifter; no breather. Overfilled? How often are you downshifting into 1st, especially "at speed"?

#3, at least, is normal in my experience. Sometimes the gears land perfectly not-aligned.

#4 is also worth at least a glance at motor/trans mounts.

 

[sgtsandman]

From the description, it sounds like either the master and/or slave cylinder for the clutch maybe failing. It also sounds like the transmission fluid is either the wrong type or is worn out.

Shifting into 1st and reverse can get tough when the fluid is worn.

As far as the noise, it sounds like pressure is building up somewhere and being released. The vents at the top of the transmission could be plugged, but that is only a guess.

 

[Caballero5.7]

My first impression is that the clutch may not be fully disengaging. The next thing is that it sounds like the atf is wrong. As if something is not allowing the synchronizers to slide or grab as needed. Does it get any better after everything heats up from driving a while?

Does your manual call for Mercon V or Mercon IV?

The manual calls for just regular Mercon, not V, for the transmission fill. My fault for misremembering. Amsoil says their ATF is compatible with both Merc and Merc V standards.

No real difference when cold vs hot, at least not that I can ascertain. Didn’t notice any real change in shift feeling after the fluid change, either. The old fluid didn’t look terrible, but definitely looked aged

 

[Caballero5.7]

I agree the clutch dragging was my first thought. Why were you bleeding it? If it wasn't fully disengaging in the first place, it's probably leaking.


Random thoughts on everything point-by-point:
There was another poster who just sourced a rebuilt HD like 2-3 weeks ago for $1300.

M5OD vents through the shifter; no breather. Overfilled? How often are you downshifting into 1st, especially "at speed"?

#3, at least, is normal in my experience. Sometimes the gears land perfectly not-aligned.

#4 is also worth at least a glance at motor/trans mounts.

I bled the clutch soon after I received the truck because of the finicky first and slow shift feeling. Same reason I replaced the transmission fluid. I have a habit of refreshing fluids when I purchase a vehicle with unknown history.

That’s great news on the HD transmission pricing, sure beats the hell out of $7k diesel transmissions!

Is it even possible to overfill the M5OD on level ground? You fill to the bottom of the hole and any extra would drain out before you re-inserted the fill plug, no? When I say “at speed”, I simply mean when slowing down to enter my driveway, or a parking lot. No more than 8mph or so. The noise/smell even happens occasionally when going into first from a stop sign. It makes the entire cab smell like ATF.

Fair enough for #3. My only real experience with manual vehicles previously have been my Fiesta ST, an F800, and a dirtbike.

I have a brand new set of motor/trans mounts lying around, though I have not taken the time to inspect the old ones.

 

[sgtsandman]

I bled the clutch soon after I received the truck because of the finicky first and slow shift feeling. Same reason I replaced the transmission fluid. I have a habit of refreshing fluids when I purchase a vehicle with unknown history.

That’s great news on the HD transmission pricing, sure beats the hell out of $7k diesel transmissions!

Is it even possible to overfill the M5OD on level ground? You fill to the bottom of the hole and any extra would drain out before you re-inserted the fill plug, no? When I say “at speed”, I simply mean when slowing down to enter my driveway, or a parking lot. No more than 8mph or so. The noise/smell even happens occasionally when going into first from a stop sign. It makes the entire cab smell like ATF.

Fair enough for #3. My only real experience with manual vehicles previously have been my Fiesta ST, an F800, and a dirtbike.

I have a brand new set of motor/trans mounts lying around, though I have not taken the time to inspect the old ones.

Some people have been known to fill the transmission through the shifter for some reason. That seems like more work than doing the fill plug, but some have posted about doing this in the past.

 

[lowspeedpursuit]

Depends on your setup, I guess. I can't imagine using the fill hole without a fluid transfer pump. They're $20 at whereverzone, but not everybody knows that. My old truck was stripper-spec and didn't have full carpet, so using the tower was trivial.

Mercon/V shouldn't really be an issue per se. It's a whole thing everybody and their granny has opinions on, but Ford doesn't make Merc anymore, so as I understand it, they reformulated V (they were originally incompatible, but now they're not) and spec that instead. For all I know that happened early enough V was always specced for your truck, or the HD in general.

I will say I think V smells like shit, and Dex/Merc doesn't bother me as much. I would rebuild the shifter and check the lower boot on the tunnel plate, since that's what seals off the cab.

 

[Caballero5.7]

From the description, it sounds like either the master and/or slave cylinder for the clutch maybe failing. It also sounds like the transmission fluid is either the wrong type or is worn out.

Shifting into 1st and reverse can get tough when the fluid is worn.

As far as the noise, it sounds like pressure is building up somewhere and being released. The vents at the top of the transmission could be plugged, but that is only a guess.

The clutch does make a squeaking noise on occasion when depressing the pedal.

The fluid is brand new Amsoil ATF, whichever was recommended by their parts finder to replace Mercon. I’ll pull up the order list to make sure it wasn’t LV or anything.

 

[Caballero5.7]

Depends on your setup, I guess. I can't imagine using the fill hole without a fluid transfer pump. They're $20 at whereverzone, but not everybody knows that. My old truck was stripper-spec and didn't have full carpet, so using the tower was trivial.

Mercon/V shouldn't really be an issue per se. It's a whole thing everybody and their granny has opinions on, but Ford doesn't make Merc anymore, so as I understand it, they reformulated V (they were originally incompatible, but now they're not) and spec that instead. For all I know that happened early enough V was always specced for your truck, or the HD in general.

I will say I think V smells like shit, and Dex/Merc doesn't bother me as much. I would rebuild the shifter and check the lower boot on the tunnel plate, since that's what seals off the cab.

I remember reading about the Merc V backwards compatibility thing at some point, which is why I was deliberating so long on what fluid to buy, since my options were a million generic multi-spec fluids, or Motorcraft Merc V for like $20+ a quart. It smells terribly strong when the smell enters the cab, can’t stand it!

I did rebuild the shifter bushing assembly when I changed the fluid. There was no bushing to speak of under the boot, just two wave washers dangling around. The new bushing came with two keyed washers and a wave, using all three made the assembly so tight it wouldn’t return to center, so I removed the bottom keyed washer. Surprisingly, this made no difference in shift feel.

The lower boot is obnoxious on the Level II dual shifters, as it’s different than the standard setup, can’t be obtained except by salvage, and is larger than normal. Even with the carpet pulled all the way up t the seats, the last couple screws holding it down have to be done blind under 6 inches of carpet!

 

[lowspeedpursuit]

The clutch does make a squeaking noise on occasion when depressing the pedal.

For me, that's enough to do the TOB, and it's most cost-effective to buy the slave with TOB attached, which takes care of a source of noise and a potential hydraulic leak. The question is how far you want to tear into things while you have the trans down.

I've always done the whole clutch and pilot "because I'm already in there" on something new-to-me. You can also do the shift rail plugs, pull the top cover, visually inspect the 1-2-3-4 synchros, wiggle the input shaft, and make the call on a rebuild. I redid input shaft shims and sent it for now on my new truck. Hasn't exploded yet. You just lose the truck for longer if you do need something, not having already ordered the parts.

If you already rebuilt the shifter, I'm not sure what might be blocking the tower vent.

So is your lower boot missing/torn, or is it okay? I have an extra flat sheet of rubber and a sheet of MLV over the shifters in my old truck. I would also switch to Dex/Merc if the smell bothers you that much and someone can confirm an '03 didn't always spec V from the factory, or the difference isn't important.

 

[Caballero5.7]

For me, that's enough to do the TOB, and it's most cost-effective to buy the slave with TOB attached, which takes care of a source of noise and a potential hydraulic leak. The question is how far you want to tear into things while you have the trans down.

I've always done the whole clutch and pilot "because I'm already in there" on something new-to-me. You can also do the shift rail plugs, pull the top cover, visually inspect the 1-2-3-4 synchros, wiggle the input shaft, and make the call on a rebuild. I redid input shaft shims and sent it for now on my new truck. Hasn't exploded yet. You just lose the truck for longer if you do need something, not having already ordered the parts.

If you already rebuilt the shifter, I'm not sure what might be blocking the tower vent.

So is your lower boot missing/torn, or is it okay? I have an extra flat sheet of rubber and a sheet of MLV over the shifters in my old truck. I would also switch to Dex/Merc if the smell bothers you that much and someone can confirm an '03 didn't always spec V from the factory, or the difference isn't important.

The lower boot seems to be in fine condition. Not sure it’s making a 100% seal to the trans tunnel, but if I take it all back apart, I’ll make sure it is.

I’ll probably see if I can get my hands on a motorcraft TOB and slave assembly. If I’m going to wind up dropping the trans, I’ll also pick up a clutch, rail plugs and rear main seal, just to do it all while I’m in there. No sense saving $100 just to have to drop the trans a second time. If it comes to a full rebuild, I’ll probably just order an entirely rebuilt unit. I enjoy learning how to fix new things, but I’d hate to booger it up and spend another 10 hours in the blazing sun. I don’t have access to bearing presses or the like to do a full teardown.

I’m excited to get to the “fun driving” part of ownership and past the “chase little mechanical gremlins” phase.

 

[4x4junkie]

Afternoon folks, new member here. I’ve been all over google trying to scrape together some knowledge but I’m coming up dry. I’ve been working on vehicles for about 20 years, but I’ve never had to troubleshoot a manual transmission. The problems I’m having are sporadic but have certain criteria they trigger in, and I’d appreciate any advice and experience from more experienced members. Sorry in advance for the essay!

I have a new to me ‘03 Level II with 195k on the clock. I fully expect things to be a bit worn out by this point. I have bled the clutch and changed the fluid with Amsoil Mercon V compliant ATF.

Issue #1:
1st, 2nd, and 3rd shifts are slow to engage, and won’t “fall” into gear until a second or two have passed of gently pushing toward the gear. I’m assuming this is synchro related, and I unfortunately believe I have the 3 piece synchros based off the year/engine. These are massively more expensive/uncommon than the two piece synchro design, and I assume they’re NOT interchangeable. I see rebuilt transmissions for sale on the internet for $1500, and judging by the fact that a 3 piece kit is $800 alone, I’m guessing that these are non HD models with the two piece design.

Issue #2:
When downshifting into first at speed, I’ve started hearing a “pssssh” like a blowoff valve, followed by the strong smell of ATF. This only happens going into first, and almost exclusively on downshifts, though it did happen the other day when I put it in first to pull away from a gas pump. I know the shift rail plugs disintegrate over time, and I haven’t checked them, but why does it sound pressurized if there are potentially big open holes there? Is there a breather tube that may be clogged? Why is it only first gear that does this?

Issue #3:
Sometimes when shifting into first, it simply won’t shift, as if there’s a blocker. Releasing the shifter and pushing it back towards first works 90% of the time. Makes red light takeoffs a bit stressful.

Issue #4:
Sometimes when you shift into first, the lever positively pops into gear, and about half a second later, the whole lever chatters for about a second, like two gears trying to mesh at speed, but I’m already in the gear??

Issue #5:
After starting the engine and ensuring the vehicle is in neutral, releasing the clutch quickly makes an “rrrrr” grinding noise for a split second after the clutch is fully released into neutral. This noise only recently stated happening, and only when the vehicle is first started. Could the rapid disengagement be pressuring the throwout or input bearing enough to make this noise? I can’t reliably recreate this except when I first start the truck.

Your issues #1 & 3 do sound like what happens with Mercon V. That is exactly how the M5OD in my BII behaved when I got it used, and also a friend's M5OD after a quik-lube place put Mercon V into his.
The tell-tale characteristic is if you hold light pressure against the stick (clutch down), after several seconds it'll fall right into gear (or if it doesn't, letting go, then retrying the shift again it'll go right in effortlessly). This would rule out incomplete clutch disengagement.

Your issues 2, 4, & 5 however seem like something unrelated to the fluid (#2 does sound like a venting issue to me also).


Getting rid of Mercon V's effects unfortunately is an arduous task I've found; simply changing the fluid once or twice doesn't undo it (seems you have to get rid of like 99.99% of it's additive residues before things might return back to normal). Maybe 10 successive fluid changes (driving 200-300 mi between each) could do it, but 4-5 changes only brought forth a minor improvement on mine & my friend's.

One thing that I have NOT yet tried (so proceed at your own risk) is to drain the trans best as possible, remove the top cover, then spray the entire insides down with a solvent (brake cleaner or acetone maybe), being sure to reach where the 5th/reverse gears are, all the bearings, inside of the gear housing, and the shifter assembly. Spin things by hand a few times while doing this (keep doing this until the solvent drains out completely clear), allow it to drain thoroughly, then leave it sit several hours with the cover off and a fan blowing on it (this to fully evaporate the solvent). Fill it with the proper ATF (Dex/Merc, or an Amsoil, Redline, or Royal Purple fluid specifically made for manual transmissions that take ATF), and hope for the best.

.. and someone can confirm an '03 didn't always spec V from the factory, or the difference isn't important.

2008 was the first year to spec Mercon V for the manual trans... But since nothing really changed inside the trans that year that I know of, I'd still use the Dex/Merc fluid (or a synthetic manual trans ATF replacement) in it myself.