Decided to set the pieces back to auto and then I'd just replace the fuses. Well, I had the generator breaker set to off, moved the level for the transfer mechanism manually to the auto position (down) and then turned power back on via the main breaker on the ATS and I witnessed a brief short across the E1 / E2 terminals and then the transfer mechanism slammed back into the upward position. I am at a loss at this point of why this would be happening.
Was the generator running and supplying the load? This would explain the "brief short across E1/E2". If not, there should be no voltage across E1 and E2, hence no spark. The switch slamming up is normal. When you re-applied utility power the transfer switch transferred the load to utility. Safety warning: Put the fiberglass cover lying in the bottom of the switch cabinet back over the contact area of the switch. It protects against arcing. Also don't ever manually operate the switch with power applied, either generator or utility, especially with that cover missing!
Things that I have noticed... when the breaker at the generator is in the on position and I run continuity across the E1/E2/comm/ground wires they all come back as connected. When I switch this breaker on the generator to off - they are all individual as I would expect - no continuity. This could be normal, not sure as I don't know how the generator deals with these feeds.
This is normal. You're measuring the stator coil of the generator through the breaker.
T1 and N1 have continuity coming from the ATS. This doesn't make sense to me either.
This might help:
N1 and N2 = Normal 1 and 2, hot phases coming from utility.
T1 and T2 = Transfer 1 and Transfer 2, Power feeding the load, normally tied to N1 and N2 unless power fails, then from E1 and E2.
E1 and E2 = Emergency 1 and Emergency 2, hot phases from generator.
Three of these are extended from the switch from the generator, fused at 5A each: N1 and N2 are used by the controller to monitor utility voltage. If this goes away, the controller will start the generator and then ground wire 23 to start the transfer. This pulls in the relay in the ATS and activates the lower transfer solenoid supplied by E1 and E2.
The fused T1 wire is used to power the controller and battery charger. T1 is used instead of N1 so that the battery charger and controller stay powered from the generator during an outage. If utility power is available T1 and N1 will be connected. If the generator is running and powering the load, T1 and E1 will be connected. Check to make sure someone didn't jumper T1 and N1 inside the generator in an attempt to power the battery charger from N1.