2008 F450 Cummins swap PCM issue

I am working on a 2008 F450 that originally had 6.4 in it. Swapped in a 1994 12v, I?m having an issue with either the CAN system is acting right or the PATS has me locked out. I can engerize the factor ford fuel pump relay, as well as energize the starter manually and engine will run. When I try to go thru the key switch, dash lights up, security light flashes some times, other times it doesn?t and when you roll key to start nothing happens. No crank and the fuel pump won?t energize. Some time the scanner connects to OBD2 others it doesn?t. Has anyone else run into a similar problem?