Sounds like your glow plugs and controller need to be changed, ehter will destroy them. The only time the Glow plug light should flash like that is after the truck starts, or maybe after you crank and then leave ignition on. Then it would be called after glow. Compared to the pre-glow that is a continuous long glow. Now this is not causing your other problem, you still need a new PMD or IP.
So if your tuned port injection had a bad ignition coil or ignition module, you would probably have similar issues, but you just have a better idea how to parts swap on those, which gets expensive when you dont understand how something works to know where to start.
Sounds like the PO messed up the truck. If he used ether then you probably need new injectors too. It easy if you have read the real GM manuals and training materials and had the drawings in them. Its not hard, just different, so don't get discouraged, its a nice truck.