mate i had the same thing.........i just put up with it for a bit. then i got stuck in water, got water in the tanks, and i had to pull them off and dry them out, when i put it back together, it started to work. im still at a loss as to how i fixed it, but if you want i can pull yours all apart and put it back together, that will fix it, ill do it for $900...........
im all seriousnes, i dont know anything about fuel systems, i think the sub pumps into the main, i reckon there musta been an air lock or something in a line somewhere and i unblocked it.
hope all this dribble helps out.........
mines a 2000 model coil cab by the way, i dunno if its the same setup as the wagon?