I swapped the entire dash and wiring into my 86 BII, donor engine came from a 92 Explorer 4.0L.
I used the 2.9L flywheel and clutch disk, pressure plate and throw out bearing, I'm using the original BII fm146/1350 and haven't had any problems with the trans as of yet and I have been beating the snot out of the BII every time I get out wheeling over the last few years, I probably get out wheeling every other weekend.
I'm running full width d44/9" spooled front and rear and sitting on 38" Swamper TSL's. I've power shifted it lots, dumped the clutch a ton and all around beat the wee out of it regularly, if it has a bad rep for being weak, I'm not sure why.
If your BII came with A/C then chances are you have the larger rad, if not I would swap in the rad from an auto equipped 4.0L.
I used the 4.0L motor mounts but they looked the same from the 2.9 to the 4.0 so I bet they will both work, the rubber in my 2.9 mounts were all cracked so I used the newer 4.0L mounts.
The 2.9L had a spacer behind the flywheel that I ended up installing on the back of the 4.0L, this spacer ended up spacing the flywheel further into the bell housing and made me have to use an auto 4.0L starter on my manual trans set-up. Had I not installed this spacer I would have had to use a manual trans 4.0L starter. The 2.9L starter won't fit. I believe the 4.0L flywheel and clutch set-up would be a stronger set-up if you have the choice to use it, do it. Mine has been OK with the 2.9L flywheel and clutch, they were brand new and what I had at the time so I went with it, but the 4.0L stuff is larger and would provide more ware surface and clamping force in the long run.
Although the through-firewall wiring connectors on the drivers side fire wall look the same, the pin layouts are different between the 86 2.9 and the ?? 4.0L. You either have to swap wires around in the connector or replace the entire harness inside and out.
The 86 BII fuel sender will not work with the 4.0L dash either, I swapped in the 4.0L sender to get the gauge working again, if you choose to go the route I went with.
Almost all the wiring connectors between the 2.9L and the 4.0L are different shape, one has round connectors and the other has square connectors, so things like the wiper motor, head light connectors and such won't connect without either changing connectors or changing components. I swapped in the 4.0L wiper motor, did the h4 head light conversion, and what ever else was under hood that didn't connect to the newer engine harness. All the components are a bolt across swap, it's just the connectors changed shape somewhere around 88-89.
Hope this helps, if you have any more questions, feel free to ask.