There are only 2 things left, the PCM and the wiring from the PCM to the coil pack. When it throws a check engine light, what codes are you getting?
In my 12 , I had a Cyl #2 misfire. Symptoms were that it wasn't always present but it presented itself, I would get the MIL lamp that would eventually clear itself only to return once the engine was under a load. My solution to the issue was 2 fold. 1st was that I had a bad PCM (driver fired the coil all the time) which caused the #2 coil to go bad and 2nd was the wire from the PCM to the #2 coil went open when the engine was hot.
You might want to sent out the PCM to someone to have it tested. I used Auto Computer Performance in Margate FL who tested mine, found the driver actually damaged the board and sold me a replacement computer cloned from my computers programming. Once I installed that, I was able to troubleshoot the trigger wiring. DO NOT use Flagship 1 or any of their associated companies for a computer diagnosis or exchange. I attached the 12 3.6L engine wiring diagram for you (which was super hard to find)