OK, lets start simple. You should have three E-pumps. Two provide fuel to the engine when the S2 is in the normal run position AND in the Aux position. One is for Aux fuel function. But all three are supposed to work in Aux position.
My generator was running fine when a loose battery terminal disconnected. The generator immediately shut down and now won't start.
Now this gen set was designed to run WITHOUT batteries. So it should have continued to run, on the DC output of the 24 Alternator. Tell us, did it stop as soon as the cable fell off? Or did it run a while? Or do you know? don't guess, know. If you are not sure, tell us.
Like Ray wrote, disconnect the E-Pumps, one at a time to find the pump that might be bad. Why might be? If the set runs in Aux mode, all three pumps SHOULD be running. If it runs in Aux, and not the normal run mode, that's kinda strange. Let first see if there is a bad pump. I would disconnect ALL three pumps, and try and start the set and make it run first in Aux, and then the normal rune modes. If the set runs in both modes, plug them one at a time into the Aux pump wire. If the first one pops the CB1, continue to test the other pumps also. Just to be sure.