Well after chatting with some LS4 guys, they recommended I go ahead and use the GM 5.3L truck engine along with the matching tranny. Mainly because it would simplify the wiring greatly by being able to control the engine and trans from the single GM ECU instead of using a standalone system, it would cost quite a bit more and would require custom programming going that route. I was thinking maybe I could just use my Isuzu ECU to control the tranny alone and using the GM one to control the engine functions, but it seems like it's more complicated than to make everything work correctly.
So i'm thinking i'll just go the truck 5.3 route since it would be pretty easy for me since my Rodeo is only 2wd, the main thing i'd need is a custom length driveshaft and mounts to make this tranny work in my rig with the stock GM ECU.
P.S. The LH6 GM 5.3 V8 has an aluminum block, not iron compared to the LY5.