If My Memory serves me right. The 2 Terminals on a VW Alternator are D+ which works just like a normal warning light wire which is usually about 2v with ignition on and goes to battery voltage with the engine running, I think that terminal is in the rounded end of the D shaped plug.

The other Terminal is DFM which is a monitoring signal and as you say goes back to the ecu.

Are you sure the Codes aren't there from the original Alternator. ? Or do they clear and return once its re-started. ?

What voltage is it charging at. ??