Starting and idling problems

Here is factory mode of operation:

The following actions occur when the starter motor is engaged.
•If the PCM receives the camshaft position sensor and crankshaft position sensor signals, it energizes the Auto Shutdown (ASD) relay and fuel pump relay. If the PCM does not receive both signals within approximately one second, it will not energize the ASD relay and fuel pump relay. The ASD and fuel pump relays supply battery voltage to the fuel pump, fuel injectors, ignition coil, (EGR solenoid and PCV heater if equipped) and heated oxygen sensors

I would check it for codes , If either cam or crank is lost it will shut the ASD off.

I agree, if you weren't having any problems with the other injectors I would put them back in and see if it runs. Seems odd if that was the only thing changed and it caused this problem.

The vehicle theft will disable the engine after 2 seconds of operation and wont allow it to crank , should leave a trouble code if that was a problem. This shouldn't be a problem with your ECM though.