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From what I've read, only the '94.5 and '95s had to be re-flashed, and if the truck has ever been to Ford service, it's most likely been flashed.
Gator, this may sound "out there", but do you have both/all doors closed? I've found that I lose connection, sometimes never get connection, just get weird stuff when I forget to close the doors. Presumably it's the dome light circuit doing something weird with the power to the port.
Doors open/closed doesn't have any effect on my rig. A/E is working correctly now that I've changed the settings to "OBD II Compliant".