This is deep.

So, my '01 360/46re, when you put it in 4lo and step on it, it will "stumble". It only does this in 4lo, yet there is no connection to the pcm that the truck is in low range that I can see.

The "stumble" must be an early form of torque management so you don't twist something apart. Maybe there is a wire going to the transfer case to tell the pcm it's in low?

Don't waste your time or money on them b.s. "tuners". I'd get a computer out of a 4wd Ram if I was you: Cost you less than a tuner in dollars and aggravation.