M5OD-R1 Input shaft bearing rattle after rebuild :(

[polymetric]

I just got done rebuilding the M5OD-R1 out of my 98 ranger (4 cyl, 2wd) with 285k. I rebuilt it because it was making the infamous input shaft bearing rattle and I figured I'd take a shot at it since a rebuild kit was only slightly more than a junkyard transmission and I thought it'd be a fun project.
So you can imagine my surprise when that sound came back after about 50 miles.
I know exactly what I did wrong, and I'm kicking myself because it was so stupid. I didn't have a depth micrometer so I used the depth probe of my calipers.
I pulled the transmission back out and checked the shaft play. Sure enough it was loose, just like the first time I took it out before I rebuilt it. Although, slightly less bad this time, I think. Took the retainer off and the shaft seal was all torn up for some reason. So maybe that wasn't in quite right.
I re-measured the clearance between the bearing and the case with an actual depth mic this time. Looks like the calipers could've done worse, as everything measured within about 0.010 of what the calipers measured. It's really hard to measure that bearing race accurately since it's so thin, and buried in the stupid integral bell housing it's hard to get my depth mic squared up on it in there. Here are my measurements, but they seem to be all over the place. I'm not sure I'm doing this right. I actually looked back at my math from when I did it the first time and I'm not sure how I ended up with the values I did...

first time (caliper)
bearing depth                  0.104
retainer depth                 0.255
shim thickness                 0.145
retainer depth after shims     0.110 (calculated)
bearing clearance              0.000 (calculated)

second time (micrometer)
bearing depth                  0.121
retainer depth                 0.261
shim thickness                 0.145 (calipers)
retainer depth after shims     0.115
clearance                     -0.006???

I must be doing something wrong because there's no way a -0.006" fit would have just turned freely by hand. But it totally did. The retainer felt fine torquing it down too. And even driving it felt fine for a while! So since the clearances were clearly wrong, and the shaft rattled around for about 10 miles before i could get the transmission back out, does that mean my bearings are toast?
What can I do to make sure I get these measurements right? I have plenty of shims to play around with.
Or should I just give up and grab a junkyard transmission? I'm just worried I'll find one and it'll have the same problem in a couple months or years. Or I could just drive it till it blows lol.

Also why the hell did mazda/ford use this godawful taper roller bearing setup anyway? Why can't it be like a Toyota where the shafts are supported in the middle like this?

Maybe I'm wrong cause I've never worked on one of those but it seems like it'd be a lot easier to work on and wouldn't have this problem at all.

Anyway, any thoughts would be greatly appreciated. Definitely a noob at transmission rebuilding. It did drive though!! Can't even imagine how tough automatics are to rebuild.

 

[broncc]

Pop the front bearing cover off and blindly add a couple thou haha. I won't say which one of my cars has an aluminum baking pan spacer, but its still running.

 

[polymetric]

I might just have to do that. I've been putting it off because I don't wanna keep putting the transmission in and taking it back out, but it's not that hard. Guess I'll be really good at transmission replacement by the end of this lol
The weird thing that freaks me out is that it was fine before I drove it for a bit. It wasn't like, I put it in and it was immediate. Which makes me wonder if I fried the bearing or something

 

[Shran]

I used the depth gauge on my calipers too for several rebuilds and considered it good enough. An actual depth mic is better but use what ya got - lots of these transmissions live long lives with worn parts, low fluid & loose tolerances.........

See if you can pull the race out and inspect it for wear. If it looks good then re-shim it and see how it behaves now that everything has settled in the case.

What are you using for sealant on the front bearing retainer? I always use Permatex anaerobic sealant... a very light layer there... RTV and stuff like that squeeze out and the blobs will break off and migrate throughout the transmission. I've torn down several M5OD's that had the oil trough clogged up full of RTV chunks.

Also some thicker sealants can throw off your shim measurements. My rule is if there is no gasket and there's a shim involved, you want the thinnest sealant... anaerobic sealant does a great job of that.

 

[polymetric]

I'm using the same thing, that red semi-transparent Permatex anaerobic stuff. Works great, I've never had any leaks and the chunks don't seem to be anywhere they shouldn't be.

I thought I figured out what was wrong with the last rebuild - When I tore it down, that front bearing baffle (this part: E8TZ-7040A)

was a bit torn up, I think it had gotten pinched between the front retainer and the case because I kinda just put it in there a bit loosely. I thought that might've thrown the tolerances off, but I put it back together, re-measured with the proper depth mic!!, ended up with the same 0.146" stacked shim, and it still rattles. this is the second time I've put it back in. I used grease to hold everything together this time, so the baffle was definitely in the right place this time.

I think my next attempt I'm gonna try to use some plastigage to see how big that gap actually is. Mostly because I'm just curious. It definitely drives okay-ish right now (after i spent 4 days bleeding that damn clutch) but that rattling is driving me crazy. It doesn't help that I replaced the exhaust with a cheap aftermarket one that bangs around at idle at the same time. It feels like I'm driving around in a giant metal trash can full of pinballs. I've got 2 different spacers and like 6 or 7 shims. I know some combination of those things will get rid of the noise. It's just that I have to put the whole damn thing together and take it apart each time I want to try a different one. My thought is if I can measure that gap with plastigage I can just add that measurement in shims. I could just toss an extra shim in there but I think this kind of stuff is the thing that really makes the difference between like 30K miles and 300K.

Thanks for all the feedback guys, I really appreciate it. Gonna try to keep updating until it's fixed for good.