Mark will tell you for sure, but I believe the only difference is the torque converter solenoid. I believe the 99 is an "on-off" switch and the 01 is a "duty cycle" type activation. You should be able to swap that easy enough. Also, don't forget the 01 is the year that they experimented with the mechanical one-way clutch (mechanical diode). That is something that will need to be upgraded if it hasn't already happened.
The solenoid body would need to be swapped, plus an orifice in the pump body needs to be reduced. In the '01 it's about 0.250". In the '99 it is about 0.030". That is HUGE difference. It will work with the larger orifice, but it will SLAM on the converter clutch so hard that you'll want to pull the trans out to fix it. I can get you instructions on how to do it if you want to.
The '01 also has a turbine speed sensor and an output speed sensor that the '99 doesn't have. You can safely ignore them. The PCM in the '99 doesn't know that they are there.
I know there are a few differences in PCM's (the early 99's had a separate BARO sensor, for instance). But would it be possible to swap in a later PCM to make the auto tranny work as-is? Maybe there are wiring differences that make the PCM swap a bigger deal than modifying the tranny (which doesn't sound like a big deal).
There are wiring differences. For example, you would need to add wiring between the PCM and both the TSS and OSS. There may also be engine differences. I don't know how the newer PCM will play with the older engine.