Did you get the powermaster 140amp grrman? I installed mine as a "true" one wire without messing with the other set up. I would have been ready to go the route you did, but my alternator excites on startup at high idle. I check my battery voltage when the car is shut off, and it is consistantly in the 13+ volt range. It sounds as though you may have crossed a wire in the 3 wire config. If the car's voltmeter is showing that it is charging, then it most likely is, as the voltmeter is not a part of the alternator circuit. Also, very important, did you make sure that the battery had a full charge before installing the alternator?
When my stock alternator was installed, the voltmeter would slowly climb up the scale as the battery discharged. Now it stays slightly below the center of the gauge, even with the lights, heater, etc. running. That indicates that the battery is staying at or near a full charge. If the battery was not fully charged when the alternator was installed, you stand the chance of blowing the diode or going thru batteries, which is why we changed to the higher amp alternator in the first place. The alternator is not designed to charge a depleted battery, but to maintain a fully charge battery.