If you are going to swap the ECU try sticking with the N body one, thats my advice cause the reason i say this is because i got a tranny from a 99cavalier for my 99 grand am and my car started freaking out, so i went and got one from an alero and it was fine so try sticking with the N body ecu, i think there are alot of differences between the 2 this was one of the mistakes i made ( dont go by the J body wireing it is different than an N body ) . I already did the work for all of you and made a post about it, i did this to my car and my car runs great i love it and its very easy to do, but like said above you have to talk to the tech about it and you have to know what you want them to do before anything so bringing info on all of this to them will help you alot, i told them what i want it and how to do it and they did it in less then 40 minutes, read about it and good luck with it.
http://www.aleromod.com/forums/showthread.php?t=20529
As for the 00 ecu when you go to the dealer all the tech has to do is connect the tec2 first and pull the vin off the 00 ecu you installed and go by that vin# then he can call the tech line, so basicly once the flash is in you car your car then is stuck with that vin for future reference, the vin thats on your car would just be for the body and the new vin will be for the motor or drive terrain. Make sure you write down the vin number from the ecu in case you ever need it.