I don't see how that would have damaged the PCM if that's all you did. But it is worth checking the coil drivers in the PCM just to be sure.
Awesome upload on the PDF!
I am thinking that the ignition coil drivers are situated in each COP (sheet 4 - "typical COP w/ integrated driver") . Correct me if I am wrong.
According to sheet 1 item 3 - "The current flow, or dwell, through the primary ignition coil is controlled by the PCM by providing a
switched ground path through the ignition coil driver to ground. When the ignition coil driver is switched ON, current rapidly builds up to a maximum value, determined by the coil inductance and resistance. When the current is switched OFF, the magnetic field collapses which induces a secondary high voltage surge and the spark plug is fired."
I believe these are 3 wire COPs (GRD/12V/PCM switched GRD). Since there appears to be no "switched ground path", there is no spark. The violet (VT) leads on each coil should have +12v via 20amp fuse (F68 - sheet 6). Per sheet 5 , one can see that 3 coils have a BLK/VT wire coming from ground (G106) and the other 3 coils have BLK/GN wires coming from ground (G107). Both power and ground sound like they have been verified.
We know that one critical input to PCM is from CKP and it appears to have an acceptable pulse frequency (>150 rpm). And it appears that CMP signal is also critical.
There are 4 CMP sensors on this engine - 2 banks, intake and exhaust. I am not certain what might happen if one of them was not functioning. Or which input pins/wires at the PCM connector houses them. The CMP signal is used to "identify the compression stroke of cylinder 1, and to synchronize the firing of the individual coils." And per sheet 3 - "Coil on plug (COP) ignition applications use the CMP sensor signal to select the correct ignition coil to fire."
Have all the signals from CMP (cam position sensors) to PCM been verified? I would consider that the next step in the troubleshooting/elimination process. All 4 are plugged in, correct?
Then we need to know what (if any) other signals might be necessary to produce PCM switched coil output, i.e. signals associated with anti-theft. This would require a more in-depth schematic of the PCM internal ignition circuit. Also, I would think if there were an anti-theft issue, it would be producing a dash indicator.