Will it make a difference what engine is input when flashing an ECM

Just for the heck of it, cuz I didn't see what engine size you did, I looked on Autozones website to see if the part numbers for the ECC (Engine Control Computer) were the same or different. If you replaced a 5.7 ltr with a 5.7 ltr? Then 99 & 2000 have the same computer. The 3.8 shows different part numbers for 99 & 2000 _______________________________________________________ Cardone Reman/Engine Control Computer 2000 Chevrolet Camaro G 5.7L SFI 8cyl http://www.autozone.com/autozone/parts/Engine-Control-Computer/_/N-9gsp8?vehicleIdForService=486281473&vehicleIdForService=486281429&_requestid=1651981 -------------------------------- 2000 Chevrolet Camaro K 3.8L FI OHV 6cyl http://www.autozone.com/autozone/parts/Engine-Control-Computer/_/N-9gsp8?vehicleIdForService=486281511&vehicleIdForService=486281473&_requestid=1651714 ---------------------------------------- 1999 Chevrolet Camaro G 5.7L SFI 8cyl http://www.autozone.com/autozone/parts/Engine-Control-Computer/_/N-9gsp8?vehicleIdForService=486281492&_requestid=1651227 ------------------------------ 1999 Chevrolet Camaro 3.8L FI OHV 6cyl http://www.autozone.com/autozone/parts/Engine-Control-Computer/_/N-9gsp8?vehicleIdForService=486281492&vehicleIdForService=486281511&_requestid=1651499 ALSO, if the engine was running fine when it left the dealer , something may be wrong somewhere else. Check connections everywhere. Do an OBD scan too.