1988 wagoneer electrical issue
I believe that your headlightsw are powered by a fusable link, likely connected near the alternator or battery, I't's possible that the wire may have dropped and did not get re-connected when you installed the alternator, or it was weak and failed while you were working.. I don't see why it would cause the aternator to not charge but either it also completes the battery circuit or there is a second wire.
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