Just a update to help the next guy out,,,
I am a Navistar tech, I was able to use my log in (Navistar DYY number) and password with Navistar's NETS to download and reprogram a ECM on a '04 F-650. The Navistar server accepted the VIN, and the file came back with the correct engine serial number. It appears that both Ford's and Navistar's nets are the same except for each has their own logo's embedded on the pages.
This truck ran rough and smoked black,with no codes. Two other shop's had worked on it before it came to us. One installed a new set of injectors, the other a new turbo. We tested the IDM (FICM)voltages @ 47.5V and installed a EBP sensor, the old one was biased, it still acted up after replacement. After the re-flash it quit smoking and ran smooth.
Thanks to this forum for helping solve this problem!