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"I assume a bad battery wouldn't case problems with the charging circuit ? "
Actually it can, but I do not think that is the case here.
How did you check the alternator ground wire? For me they failed (mostly) inside the ring terminal on the chassis side and the failure is almost impossible to see. The rythmic "flashing" of the warning light is completely gone? If not, sounds like the wire portion of the ground wire is making intermitent contact with the ring terminal as the engine naturally moves a little with each rotation.
Only way to know for sure is remove the wire from the alternator and chassis side to inspect it off the car.
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