2003 Malibu wouln't start but now it will

While we were troubleshooting the car I pulled this forum up amd received information that led me to finding what was causing the car not to start and getting the car running. You notice I did not say fix the problem and I'll tell you why. I''l shorten the story by telling you that we did the following in this order: emptied the fuel tank and replaced with known good fuel. Pumped good fuel to the rail and tested pressure at 53 PSI. Changed spark plugs and wires because they needed it anyway. This blog led me to the computer and how to test pulsing the injectors. In preparing to do this we noticed that a ground was missing at the 10 pin connector. We got a diagram from Autozone and verified the wire color of the input ground to the PCM. We did not unplug the computer but pulled it out enough to get to the wiring. Input grounds tested okay. We then tested output grounds at the 10 pin connector by cutting into the wires. All wires pulsed properly and this surprised us since we expected this to fail. We plugged the connector up and started the car. The PCM has the capability to turn the ground pulsing off if the conditions warrant it. Is this car's PCM engineered to do this if through a sensor, it detects a condition that could damage the engine? In the process of troubleshooting, we unplugged everything we needed to remove the plenum cover to get to the injectors. We also removed the TBS to test for a ground because the wire on the TBS was the same color as the wire missing ground at the ten pin connector. All we know from this is that the PCM was not pulsing ground and that was the reason the car would not start. And we know that somehow the PCM began pulsing the ground and the car started. Could we have changed an input to the PCM that allowed the PCM to pulse properly?
Thx
Terry

If the PCM was not pulsing the injectors on startup, chances are the PCM did not receive a fuel enable signal from the Theft Deterrant system....check for a code B958 or B2960...if present, that is your problem.....usual problem is the PassLock sensor, or connection at the BCM.....