Any idea of the charge situation of the battery? If you don't think it was down very far, the next thing is to find out what the output voltage of the alternator was. In other words, is it being controlled by the VR, or is the VR bad?
So fire it up and measure voltage at the battery. Should be no more than 14 normally, and an absolute max of say, 14.5. That itself is higher than normal
You likely made a wiring error causing the alternator to charge full tilt. The newer ISOLATED FIELD (incorrectly, "dual field") has the blue at one field connected to switched 12V power, AKA the key side of the ballast, and the other field is green, going back to the VR. VR MUST be grounded