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If the diodes are bypassed (shorted) anywhere, would'nt that produce reverse charging? I remember experiencing something like that once.

Simple. The interior poles are reversed in the alt. That would reverse the DC current.

Sounds like your altenator is wired reversed to me. If you say it runs fine "without" the battery hooked up and drains it when it is, your altenator is sucking and not adding voltage.