Start an die conditon
Did you do anything with the PCM when you reinstalled the engine? It's possible that it isn't getting that fuel enable signal although one would think it wouldn't run at all in that case. It could be that the SECURITY light is just a coincidence and you just have a run-of-the-mill engine problem such as fuel starvation, bad spark, timing, etc.
I suggested that the SECURITY light may be a coincidence because the car will start and run (although not well) which would indicate that the light is on due to a VATS fault which was detected while the car was running. When that happens, VATS will allow starting on the assumption that it's a fault rather than a theft attempt. If it was VATS causing the problem then the starter would not turn at all and the fuel would be completely cut off so no amount of jockeying the pedal would keep it running. Add that to the fact that it's a new/rebuilt engine installation and I would guess that it's something unrelated to the security system.
Both my son's Firebirds had to have the VATS bypass. On mine, the security light came on one day as I was driving. It's been that way for about 10 years with no other issues.








