I switch them around all the time...here are a few issues I've run into.
Vin numbers are different, and it pisses off the emission station people.
03 only work on 03's. 04's only work on 04's trucks and 05 excursions. A 03 truck will start, run and drive with a 04 PCM, and vise versa, but there are few things that are different. One of them is engine fan circuit, and the Tow/haul indicator won't work.
Some trucks do not have 4 wheel ABS, usually cheaper XL's.
Swapping a 05 to a newer truck works, but a 06-07 to a 05 can cause issues if the 05 was one of the ones built w/o a MAF sensor.
One thing I've noticed when going back in programming is the trucks that get programmed to ignore the EBP can run like crap after they get flashed back because they need a new EBP. One of those deals where that was the dealer fix ....."just flash it"
As for the other questions....We'll have to wait for Bill or Cody to answer.