01 grand am crank but no start

Daughter was In drive thru when grand am started running rough then died. Had towed home. Scanner showed cylinder 1, 3 misfire and also B2965. This grand am has the 2.4l so I pulled the ignition cover, left plugged in and inserted plugs. Cranked car and all plugs sparked. When key turned forward I hear the fuel pump priming. I changed fuel pump last month so it has to be good. So I went the direction of the B2965 which is key in ignition open circuit. I replaced the ignition cylinder and didn’t help. Today I replaced the ignition housing. Didn’t work. The car already had the security mod to it so the security light goes out several secs after turning key forward. Scanner shows no more B2965 codes and also shows key in ignition with pass lock good. I’m at a loss of what else to look at. Car was running fine before it died.

Just because the pump is running doesn't mean injectors are firing. Just because you have spark doesn't mean it's firing correctly.

Unfortunately it's going to take further diagnosis. It could be physical timing out of whack. It could be ignition timing out of whack due to a cam sensor or something. It could be the injectors not firing due to a sensor failure.

for shits and giggles I swapped to the old pump to see how it would run. I noticed when I removed the fuel line from the pump there wasn't much pressure. Tried starting it and did nothing. So I swapped back to the new pump and still didn't have any pressure when removing the fuel line from pump. Read about the fuel pressure regulator and to remove the vac line from the top. did that and it started right but running rough. Did live data on scanner and showed cylinder 2, 3 with misfires. so I thought removing the fuel pressure reg and a coil pack should fix it