Didn't realize he was swapping the tranny too, must have missed that part. The tranny swap does make it alot harder, motor swap alone though, isn't too bad.
Yeah if the transmission was a manual he would have to swap the entire wiring harness out of the truck, becuase the PCM runs everything, from the glow plugs, to the throttle sensor on the pedal, to the engine, etc. At this point, given the fact he's working with a 93 4L80E, he'll have to find a 94+ transmission and on top of all of that would have to re-wire the entire truck. So in this case the best route would be to rebuild the 93 6.5, or find a old 6.2, any pre-93 cable driven diesel, not a 94+ drive by wire.
IMO, i think anytime you swap a complete wiring harness, you are setting yourself up for a electrical disaster down the road if you had issues somewhere.
It sucks because you wouldn't think the 93 and 94 would be that different... i'd just hate to see him rip the entire truck apart and make a giant mess with two perfectly good vehicles haha.