It got from NM to your storage ok so would that say the wiring is not backwards?
Ignition (run circuit) only from house batts and not from engine batt suggests the AUX start switch is closed somehow. There would not be that much of a drain on the house batts so they would be dead after a week in storage, so that is odd.
Do you have the three-way AUX dash switch or no dash AUX start at all, and you just get the house batts and engine batts in parallel every time you turn the ignition on? (My Class C is like that, but others have the more complicated three-way set-up--it could make a difference in what might be wrong there)
(We had a thread or two about all this dash switch business a few months ago if it is relevant)
Going back to the alternator failure, it can happen if the house batts are so low, and the engine batt is not in the picture to make the alternator voltage drop to a float voltage, that the alternator keeps putting out high amps to the house for so long, the alternator gets too hot and fails ( something like that anyway)---so I wonder if what is happening now is from the same thing that went wrong back then.
1. 1991 Oakland 28DB Class C
on Ford E350-460-7.5 Gas EFI
Photo in Profile
2. 1991 Bighorn 9.5ft Truck Camper on 2003 Chev 2500HD 6.0 Gas
See Profile for Electronic set-ups for 1. and 2.