I think you're going to have to stick to the LST drivetrain... Trying to mod another drivetrain from another MT would be pointless when you have one that is a perfect fit to the chassis! I'd suggest you buy LST diffs and CVD's etc, and use all the availible upgrades that were designed for that truck (alu diff cases etc).

You'll end up with something easy to work on, reliable and relatively cheap. It sort of ruins the whole "design & build it yourself" concept, but at least you will end up with a good truck.