Your BII only has the BW1354 case if it also has a dana 35 ttb, not the dana 28.
Many 90 BII's did have the Dana 35 up front, but not all of them.
the only difference between the 1350 T case and 1354 is the yoke for the front driveshaft.
The 4.0L SHOULD have been installed in 4x4 Bronco II's. Dont get me wrong the 2.9L is a kick ass engine, I loved mine, built it into one mean mother too...but the 4.0L has the TORQUE. You should have seen my face the day I fired up the 4.0L for the first time and took it around the block.
I have a 93 OHV with approx 190K miles on it, I converted to an automatic and now have a fully custom built automatic, I have a 8.8 rear end, 4.10 gears and 33" tires and my BII hauls ass! It also tows a 19' boat without an issue.
I spent a good year researching the conversion as well, only a few had done it before me, I learned alot the first time, but I spent another year getting it right (cruise control working, A/C wiring, etc etc..) Since then I have done the wiring for several different years and I can tell you what each wire iunder your hood does, where it goes and why, for all the different years of the OHV. DO IT! You will be happy as a CLAM. 4.0L + BII = FUN to drive