We have been doing cummins repower in Ford, GM, medium duty truck conversions for years now.
We've done several of the ifs body style GM trucks, 88 throught 2001. The 88 to 96 models had no problems going in, we had nothing but problems with automatics in these though. The 400 trannies came apart in a few months when we tried to use them for pulling.
If you really want to use a GM automatic, try locating a used GM p-30 like a bread truck or Fed Ex truck. These have 4 bt engines in them and t400 trannies. The brackets and adpaters in these trucks will bolt right up to a 5. 9 and any GM auto. We have also used these adapters to install 5. 9's in 1997 and older GM trucks with 4 speed trannies. You have to gear them really tall in the rear ends, or put a Gear Vendors unit behind them. It makes ithe 5. 9 nearly a drop in unit. Espec ially in 2wd trucks with 6bt's ( 6bta's require some refits like moving the the transmission back a few inches.
Only thing I had issues with on the ifs trucks were the headlight assemblies had to be modified in order to fit the inner cooler between them. I did not like this as I try to make everything a bolt in setup in the event of an accident like hitting a deer. Insurance adjusters are hard enough to deal with on a regular equipped vehicle. Try telling them to modify all parts before they are replaced, they'll just total the truck out then.
We stick to NV-4500 and NV-5600 transmissions now. This not only is a proven set up, but you can get off the shelf parts if something breaks.
If it is 4wd, Dodge 241 transfer cases will drop right in with minor adjustment to the 4wd shifter length. You'll need the Gm style sensor for the 4wd engagement. You can also use the GM nv-4500 trannies if you change out the input shaft. Some NV-4500's will be different that others in GM trucks. I believe it was something with the hydraulic clutch and slave cylinder set up. There are different assemblies in certain years. Those are a problem.
Good luck.
If you have questions, please post them here, don't email me directly, I hardly check the account that I listed for this forum, it hardly has any storage either.