The 2.9 uses a 8 7/8 inch clutch. The m50 uses a 10 inch clutch. You will need the flywheel for a 4.0 and the engine plate also. Grab the positive battery cable if available. There are 2 wires on the 4.0 starter. There is an automatic and a manual starter also. I used a 1990 Ranger Master and slave cylinder for 4.0 when I did the switch. I found a 1993 Explorer complete so I had everything for the changeover.
This is from the Tech archive, and seems to suggest that I would not need to replace the flywheel. I probably will, just like to understand everything before I start a project:
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Replacing a Manual Transmission with a different Manual Transmission:
All 2.8, 2.9, 4.0 V-6’s and transmissions are the same. keep flywheel, bellhousing, pilot bearing, throughout bearing, clutch release mechanism(s), flexplate, torque converter with the transmission.
The only modification that will need to be done is to the floor plate. You can either cut it to fit the new shifter or you can remove the front seats and pull the carpet back to get to the (4) 8mm bolts that hold it on and swap in the one from your donor. All that may be left is to trim the carpet. If you take your time, the piece that you trim out can be used to replaced the gap it will leave behind the shifter."