OldSchoolFormula

Hi guys, having a bit of a problem here with PCM's and codes. I have a 2001 LS1/A4 in my '73 Firebird. using the original PCM which I had sent out to a guy, the car runs wonderfully except for the fan temps that were never adjusted, and the fact that the fuel tank pressure code was never deleted. Anyway, the guy who did it took several months to get the PCM back to me, so I did not feel like sending him my PCM back as this car is my daily driver. So, I order up a PCM from another guy who deleted the codes I needed deleted and reset my fan temps. The old computer would simply throw a code for the pressure unit, but the new PCM throws both P1133 and P0300. It misses bad when cruising in OD and causes the converter to unlock. In the first 3 gears, no problem - it runs great. Anyone have any idea as to why two seperate computers would be so different in detecting (or inducing!) a misfire? I can run them back to back, and the miss is only apparent with the new PCM. Could it be the flash on it is for a milder motor than the LS1, like a 5.3 or something? If so, why doesn't it seem lean in the first 3 gears?

Would appreciate any help.