When my 110 amp alternator failed 8 years ago I replaced it with a rebuilt 180 amp one. I has worked fine and then I installed an ammeter/voltmeter with a shunt to measure amps and volts to the house batteries. I never measured more than 7 amps going into a 50% discharged 2 6 volts GC batteries. After reading your post I wonder if some strands of wire were chewed or worn through reducing the amps going into the batteries. I would assume I should see more than 7 amps under those conditions. Something else to check.