Making progress. I am not a Cummins expert by any means, just throwing some suggestions out there.
When you say that with the can lifted above the pump, which I think is causing a siphon effect, and fuel comes out of the priming plug hole, is this true with the engine off? If it's flowing pretty freely without the pump turning then it sounds like the gear pump may be pretty worn.
I'm not sure but I'm guessing the pump housing is open to the suction side so you need that priming plug screwed in to make a valid test?
I'm thinking it's sucking air somewhere on the pump and there's only so many possibilities. If it's not leaking fuel anywhere obvious then that leaves the drive shaft seal, throttle shaft seal, if it has one the tach drive seal, and if it has the AFC where a line from the intake manifold attaches you may have a hole in the diaphragm. Try removing that line and plugging the port, see if that makes a difference. If it has a tach cable take that off and find a way to cap the drive with a piece of rubber or like that with a hose clamp maybe? Usually if a gasket or throttle shaft seal is leaking you'll see fuel coming out somewhere, but seals do funny stuff sometimes. If it's a drive shaft seal, you might be getting some fuel in the oil pan also. Gotta be a pretty good leak if it won't suck fuel from a can on a short hose. Good luck.