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If you didn't have a good ground through the chassis to the engine and battery, you might have zapped the new alternator diodes.
The voltage regulators are specific to the type of alternator, I believe. The Haynes manual takes pains to treat each type (SEV-Marchal vs. Motorola, I believe) separately. You may have a mismatched setup, however, even at the discount store, the parts guy asked me which type I had.
Only other thing I can think of without tracing through the circuits is a shorting ignition switch.
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