So I have a 2012 Countryman base engine (also have a 2017 S) anyway I hadn’t used the 2012 for a couple months and battery got low. I recharged it and it seems fine. However after starting I got a charging system malfunction warning and the vehicle shed some load by killing the blower motor etc. I metered at the alternator output wire to battery and it was only battery voltage which was 12.5v or less as battery discharged. Back pin metered the single small wire going to the voltage regulator on the alternator and had like 6 volts. So pulled the rad support and replaced the alternator with a remy rebuilt unit. When I started the warning was gone, however the alternator doesn’t seem to be charging. When I meter the output wire it isn’t 14-16v it just seems to stay at battery voltage and slowly drop while car is running at 2000rpm with headlights on and AC. Blower fan was okay at first but then went to like a low speed even though on high. Back pin metered the small wire going into voltage regulator and there was 0 volts. Battery voltage dropped from about 12.5 volts to 11.4 while I was testing. No engine faults showed on my autel scanner/reader. Does anyone know what that wire going to the voltage regulator should read with the car running? Could I have lost my field winding charge in shipping? This car has that sensing system on the negative battery wiring as well which should be telling the DME/ECU what the battery voltage and temp is. I have a manual but it doesn’t say much on the charging system. If anyone has a wiring diagram or can give some info it would be appreciated.

Borrowed a snapon scanner and registered battery as if new however didn’t fix the issue. I could see with snapon scanner that there was no specific IBS fault or DME fault. Did have 2 alternator faults stored 2E24 generator electrical fault and 2E34 generator machanical fault. Couldn’t find any more info on those codes. Suspecting the $400 rebuilt alternator is faulty.