Just found this at the Association of Diesel Specialist's...
This 2004 F-250 that had a issue. This was a 6.0L that would not crank, reflash or run self-tests or program the PCM either. I have learned that these two engines use three connectors wired to the PCM. There is an engine connector, body connector and one for the automatic transmission. The PCM will operate but not display any PIDS or scan data if you remove the engine connector on either model.
Upon disconnecting the engine connector, the PCM became responsive and would run the self-tests. The PCM also would allow program updates from the IDS scan tool. In other words, the PCM acted normal with the engine connector was disconnected. When you reconnect the PCM, cycle the key, the PCM would become unresponsive, display blank PCM message all over again.
The 2004 F-250 was repaired by replacing the crank sensor, the engine harness and the PCM. We concluded that there was a short in the harness that partially shut the PCM down. We had found the crank sensor was not responsive and the harness had a short. The PCM was damaged from the short.
Looks like a good place to start !!