2002 No communication with PCM

Hello everyone, I have a 2004 model cab that had the 6.0 engine in it. I just finished a 7.3 swap in. Let me start off by saying this is not my first swap so I know what all is involved with it (having to swap all wiring etc.) I had a 2002 donor truck that ran and drove perfectly that I got my engine trans transfer case and all my wiring from. I just finished up the swap a few weeks ago and since then I have been fighting a no PCM communication with scan tool. I have no fuel pump, no glow plugs, no IDM. WTS light comes on, CEL comes on. Im getting power at the OBD2 port, and power at all the power pins at the PCM, so I know the pcm is coming on butits not ending out signal to fire up the IDM and other components. I know its not PCM, IDM, or fuse panel related because I have sent all 3 off for tesing/repair and all came back good. Im almost 100% positive that its not a wiring issue because I have spare harnesses from other donor trucks that I have swapped in place to try to find the issue. Im confident its a problem in the 5vref but I can not find the problem Ive gone as far as unplugging the engine harness all together just to try to get power. I have had no luck and exhausted every option I know. Fuel bowl has been deleted no so heater, all battery cables are brand new with brand new batteries. If anyone has any advice PLEASE HELP!