If you install the 1999 engine, engine harness and PCM then your sensors, wiring and PCM will all be compatible with each other. However, your new PCM will not be compatible with the other stock PATS components (keys, anti-theft transceiver module and possibly remote anti-theft personality module). I'm not very familiar with PATS so you should determine what modules are required from the donor. Getting the ignition keys and cylinder lock may save you a tow to the dealer for reprogramming.
I think most of the swaps that have been done are either prior to PATS or the stock PCM was retained with a minor sacrifice of optimum performance.
The exhaust configuration may also be different (series cats vs parallel cats). I suggest that you determine all of the work and costs before starting the project. It may not be worth a gain of 50 hp. Do you have another vehicle to drive while the swap is in progress?