the 90-94 4.0L is th best donar because of a few things......
1. wiring issues and only one O2 sensor
2. they are a direct dolt in to the 2.9L
3. you can use your fly wheel with these years, as long as you match the starter to the selection.
I don't think you can use the flywheel from the 2.9L on the newer 4.0L's they did a big overhaul to the design I think you are talking about.
Is the 4.0 short block similar enough to use the 2.9's intake, etc.? Would that even be a consideration?
from what I hear, no. while they are in the same block family the top ends will not swap.....on top of that if it did you will have a problem setting the timing.....the 4.0L uses a distributerless system and the 2.9L uses a distributer. other bonuses are the 4.0L is MAS air and the 2.9L is not.
I have heard that you can alter the bell housing on the original tranny to fit this motor.......but this is where I dissagree totaly with this swap. your tranny is only rated to hold around 170ft/lbs of torque. while the 90-94 4.0L is around 220 this motor is more then that. so, you are really already pushing your luck with the 90-94. while I had no problems out of mine I also used the 2.9L flywheel for one reason......I would rather replace a clutch then have to rebuild or go threw the hastle I had trying to find a new tranny. if you are planning on doing a motor swap I say go 5.0L but if you are on a budget then the 90-94 4.0L is the one you want. I enjoyed mine alot, and didn't regret it for one minute.....but I was only trying to keep mine on the road untill I could go for the 5.0L. now I have a 351M go figure........if you need any help just post up I will help you with what I know.