What are the differences in the 1996 to 2003 46re's that effect interchange?

In late 2000 they changed the governor pressure solenoid (and harness), and also changed the resistance of the internal thermistor, which is used to determine the transmission temperature.

Not sure if there are other changes.

The solonoid is the same, the temp sensor/pressure sensor is different, if I am just trying to swap one I cut the end of the harness and splice it in so I can plug in the apropriate sensor. Also in 2002 they put a bigger hole in the case for the bolt on neutral switch and no threads to thread in the old one. Some models bolt the T-case shifter to the case and some to the floor, the floor mounted ones don't always have the bosses drilled and tapped for the case mounted ones, I do not remember the years but have had to drill a couple out.

I have never seen a 2000+ with the old sensor.