Stumped

I am working on a 01 that we pulled the engine out to reseal, stud and put a small set of twins on. Tried fire it today and couldn't get the fuel pump to run, it has a Raptor pump on it. So I took it out cleaned the motor that was slightly dirty from brush dust hooked it up to the battery with jumper wires and a 10 amp fuse and it worked just fine, so I reinstalled to the truck wiring and it makes a little noise then the relay clicks. So I stole a relay from a different spot and it didn't make a difference, so I ohmed the power wire back to the relay and it had minimal resistance. If I understand this the ECM controls the pump via the ground, is there any good way to check ground through the ECM? I think the ECM might be fried, when they were hooking up the cables at the fuse box one of the guys helping took the small ground wire from the battery cable and tried to hook it to the alternator feed thus destroying the ECM in my opinion. Any help would be great.

Thanks Don.