OK guys, regarding this nightmare with the gear swap and PCM programming, I have an idea to try but I want to run it through here and see if anyone can think of a reason why this wouldn't work...
I did some searching online, and found another 2004 TB SWB in a salvage yard with the GT5 gears. They were kind enough to provide the full VIN, and a picture of the glove-box RPO code sticker, verifying that it really does have the GT5 gears. Of course about half the other RPO codes differ from my own vehicle, so its not an exact match.
My question is, does it matter? Both vehicles have the 4.2 engine and are 4WD. They also both have the U68 code for the DIC (which could potentially be an issue?), so they seem to be a good match for what seems like the most critical parts.
Most importantly -- If I have someone pull the programming from this VIN and flash it into my PCM (then change the VIN in the PCM to match my vehicle again), is there any reason why I would have any problems? Would everything work like from the factory at this point? Or do any of those RPO codes signify actual changes to the programming other than minor things I could correct by copying tables back from HPTuners?