There were 15 CP vehicles, there were 5 PB-1 cars, and 12 PB-2 vehicles. CP stands for Confirmation Prototype which is the level of prototype at which most of the engineering validation is completed. PB-1 is the level of prototype at which the engineering is done, and the car is nearly ready to be built, where manufacturing validation is done. PB-2 is essentially ready to go, the final level before production begins.
That's a total of 32 pre-production prototypes. Some of these cars are in museums, some were destroyed (probably 5-10 were destroyed, but I can't verify that exactly at this time), one went to Stillen, one went to GDG, 2 of them went to Saleen for manufacturing trials, Ford Racing has one of the PBs, two PB vehicles are also verifiably gone, and public affairs has at least 1 in Europe. These are the last of SVT's PB vehicles. After they are gone, they will have none left.
All 15 of the CP vehicles had 2004 VINs.
There would literally be pages of differences. Most of this stuff is really detailed stuff like squeak and rattle changes, electrical, chassis changes, the magnesium cross beam, the restraint control module, the passenger mirror got moved rearward...all kinds of stuff. Lots and lots of fine tuning between PB-1 and 2.
5 PB-1, 12 PB-2.
There you go. That's what I've got for now. Disclaimer, these were all (fairly detailed) off the cuff answers so they aren't written in stone.