I had the same question this spring when I swapped a 2005 Tap-Shift tranny into my 1999 GTP. As stated earlier, there are differences but it can work. Being 2003+ the transmission has a different electrical connection scheme at the harness plug. It also has a different pressure control solenoid and a very abbreviated manifold pressure switch assembly, compared to earlier model years.
I found that there is more than one way to skin this cat: Change the harness wiring scheme and iron out the wrinkles with your current PCM or Simply run a PCM from a 2003 GTP (GM P/N 12209624) and leave everything else alone. I chose the second option because it would address both the control signal differences with the new style PCS valve and the wiring changes with one swap. Plus everything was plug-and-play. Just put the existing range selector switch onto the new trans and plug in the 2003 GTP PCM.
The valve body differences between standard and Tap-Shift don't amount to much, P-R-N-D ranges are entirely identical between the two. I worried that selecting the 3-2-1 manual ranges would cause problems but everything works just like normal. Those manual ranges have a few circuit differences that seem to tailor the Tap-Shift trans for faster hydraulic actions during manual shifts but still perform normally without Tap Shift control.
Mine is a Tap-Shift trans but still has the 2.93:1 final drive, so I needed zero trans parameter changes to have a fully-functioning 2005 Tap-Shift trans running in a 1999 GTP using the 2003 GTP PCM. The trans adjustments that I have made are for driveablity with my cam.
Yours would require some custom program work in the PCM to accommodate the 3.29:1 final drive. But that's pretty easy if you know what to change.
P.S. That same 2003 PCM is also working very well on my 2007 L32 engine with the mods listed below and some custom tuning. It was $25 shipped on ebay and included the factory plugs that I need to build an outboard flash setup.
