Have you checked the resistance of the field windings in the alternator? It's possible a brush lead got shorted, or even the rotor itself might have developed a short. Resistance at the Field terminal of the alternator should be above 2 ohms, possibly more. Also, disconnect the field wire at ther alternator- - - -you should read a completely open circuit between the regulator connector and ground with the F wire disconnected at the alternator.
Jerry