ECU Difference between 1999 and 2000
 

So why is it i can buy the immobilizer bypass for $675.00 for a 99, but can't for a 2000 ? What's the difference between the two cars?

Probably a good question for ECUDoctors - http://www.ecudoctors.com/
I believe it is a difference in the ECU/DME programming. One can program the 98/99 ECU/DME to ignore the required input from the immobilizer, but that was changed in the ECU/DME 2000 and beyond.

So i wonder if i can swap the 2000 ECU, for a 1999...

You might have to get into the technical details (pinout details as well) to find the difference...also call the ECUDoctors. They are usually very helpful. The main difference might be in the management of the vario-cam versus vario-cam plus in later cars, as well as the Motronic version and ABS/PSM management. Why are you trying to bypass the immobilizer?
99 ECU http://www.ecudoctors.com/porsche-99...261204605.html
2000+ ECU http://www.ecudoctors.com/porsche-99...261206579.html

I would like to ditch it because for me, i would much rather have $10.00 dollar keys, a $400.00 alarm with remote start, and any other option i can dream up that is easily serviceable for the rest of my life, VS $400.00 Keys, and a very expensive box that is somewhat flaky, and is installed in the most water prone spot in the car.

I would ditch it in a second if i could

According to "The Definitive Guide.. to the 996" - 2000 is indeed the year that Porsche switched from Motronic 5.2 to 7.2.

So drive by wire i guess.... That sucks, looks like 99's are the cars to buy. You get the dual row IMS bearing, and can get rid of the immobilizer.