I have found out that the stock gages will work if you use the stock input sensors through the ECM. The only hang up is the tachometer, but that is still being ironed out.
I also believe the 231 T-case will handle the torque of the stock 4bt, I say stock because who knows how far someone will push the envelope.
I sized up a 79 Bronco 9" rear diff. it is 65" WMS-WMS. The stock TJ D44 is 60.5" IIRC. I think the D44 is a good strong unit, but I came across this 9" with a Detroit locker at a price I could not refuse. So this may very well get used full width with some offset rims.
The D35 front I feel is lethargic at best, especially after adding bigger tires and the weight of the engine.
I saw one 4btTJ where it was manditory to use a "center outlet" exhaust manifold, I was told it is needed but I have not fit my engine into the TJ yet to see if there is a way to use the standard rear outlet manifold.
I saw it mentioned that dual fuel pickups may be needed after removing the stock gas fuel pump due to no baffeling in the tank. I agree dual pick ups will be better than one but I doubt it is necessary. I have seen no stock light truck diesel fuel tanks that employ baffels and they are not having fuel starvation issues. Albeit with after market fuel pick ups we don't run them real low on fuel. am involved in several high performance diesels and some have used sumps, but this leads to issues with sucking garbage from the bottom of the tank.