I've done a similar auto to manual conversion, but mine was on a '90 Bronco II using a '90 Ranger for the donor (both 2.9L and 2WD). So close but not the same as what you're doing.
I did read that the 4.0 and 2.9 have different-sized flywheels. I find that strange since the bellhousing is integral to the tranny and therefore share the same bellhousing size. Does anyone know what issues I may encounter if I attempt to use the 2.9 flywheel on the 4.0? I'm guessing it simply wont bolt up...
The 4.0 had more power than a 2.9, so it has a slightly bigger clutch than the 2.9 (by 1", I think). As far as I know, you should be able to use either, but
you'll need to use the parts as a set for whichever application you choose: flywheel, clutch disc, pressure plate, slave cylinder (this might be the same), starter, and the indexing plate between the motor and trans.
I'm not sure that if you change to the 2.9 starter if it will require any wiring reconfiguration (seem to remember some difference).
The flywheel bolt configuration should be the same between the year models you've got.
If you don't beat the truck too hard, using the 2.9 clutch would work, but all things considered keeping the original clutch setup would probably be better.
Clutch safety switch: How to handle the switch which cuts starting system until clutch is depressed? Is there a harness I can connect to if I have the pedal switch?
Yes. Just make sure that you keep the switch ("Triple Function Switch") on the donor's clutch pedal and master cylinder. There should be a connector for the clutch switch in the auto harness on your truck already, taped up above the pedals. It'll have a shorting jumper plugged into it for use with the auto; just unplug the jumper and then the remaining connector will plug into the clutch switch on the newly added clutch pedal.
The cruise control will still work if you install the triple function clutch switch.
The only other wiring that comes to mind, was the short harness underneath going to the transmission, for the reverse light switch. On mine all I had to do change out the original auto short harness for the donor's manual short harness.
I believe the ECU controls the OD in the A4LD but this won't be needed in the manual set up. Are there any errors that may prevent motor from starting?
From researching to do my swap, I believe that using your original ECU will still allow the motor to run, but you'll have a higher idle and a CEL from the computer not seeing the OD solenoids. Your best move would be to get an ECU for your engine size, year model, and same emissions. Not sure, but emissions may be just whether with EGR or without EGR. On mine the donor EM just plugged in with no issues, but again mine was 2.9 / 2.9.
Is there anything else I'm missing?
Grab the transmission tunnel floor plate from the donor. It'll be easier than hacking up the auto's solid floor plate. Don't forget about the rubber boot for the manual shifter.
Manual steering column can be swapped whole from the donor, or you can rebuild yours using the donor. Some people just remove the auto shifter, but it's not hard to make the steering column correct for a manual. If you go this route, also grab the blockout plate to cover the "PRNDL" indicator in the cluster (it goes in easy).
There's a ton of info here on TRS, which is easy to find using the "search" function. It seems that there's several posts or tech articles which cover upgrading a 2.9 to 4.0 clutch upgrade which may help you.
Hope this helps. If I'm wrong on anything, hopefully somebody will step in with better info.
Good luck!
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