Have a weird problem

[starcommtrey1]

I had standpipes, dummy plugs, and a stc fitting installed into my truck. When they put the truck back together, my OBDII port would no longer allow them to connect. The truck also is a no start. Long story short, the CAN network is down in the truck. Swapped engine harnesses, disconnected all components and still nothing. My SCT could change my engine tunes and see ECT and EOT and voltage, but that was it. MY SGII, Ford INS(the computer that hooks to the red thing, uses internet and has troubleshooting trees), and the mechanics scanner could not communicate with the PCM. We eliminated from the PCM to the components as being the problem. On the first cannon plug that runs to the truck, all grounds were good except the PTO, but being I do not have a PTO I figured that is why. All the other pins were open. On the last port that is the smallest, all the pins were open. I need someone to point me in the right direction, as the mechanic, Ford, and I am now all at a loss.