interesting question
What year body are you going to use?
Just a few comments with very little thought:
The 3rd generations came with the SOHC V6 and the 5R55S. The 2nd generations came with the 5R55E and either the SOHC or OHV V6. Because of solenoid differences (and other things) you would have to use a 3rd generation PCM to control the 5R55S/W.
The 2004 and later 3rd gens have electronic throttle control and pulse width modulation control of the fuel pump referencing a pressure sensor on the fuel rail. There was no production OHV V6 with those capabilities so you should limit your consideration to a 2002 or 2003 PCM for simplification. I'd have to check to see if the 2002 and 2003 have the same fuel pressure and injectors as the 1998 and later OHV V6 with a returnless fuel system.
The OHV V6 uses a synchronizer to determine if a cylinder is on the compression or exhaust stroke. The SOHC V6 uses a camshaft position sensor for the same function. The sensors may have different electrical characteristics incompatible with the 3rd generation PCM depending on the year of the OHV V6.
The early V6s had a 6 bolt crankshaft flange but the SOHC V6 has an 8 bolt crankshaft flange.