Engine/Transmission (1998.5 - 2002) Code and associated issues?

[Scrappy]

My Father has an '02 3500 HO Cummins, He replaced the LP with a FASS about a year ago. After the FASS he was still having the fuel pressure issue and the associated codes for the VP 44 so it got replaced this spring. All was good until this week, it starts normally and runs fine for about a mile. After the mile or so it starts flashing the WTS light and stumbles(or the light comes on and the truck dies) it does this until it warms up to operating temperature then all is fine. He was able to catch a 1694 code once but the dealer can't recall it. I thought it might be a loose/ corroded ground and he is checking them out. What else could be wrong?

 

[Scrappy]

Update;

when the light fashes/comes on, so do all the other lights that light during the startup sequence. It is like the key is shut off and turned back on. Of course the dealer could not find anything wrong even though it did duplicate.