there is a small wiring harness on the alternator. it should be two tiny post studs in the middle and a larger one on each side. if you follow the negative battery cable to the alternator you should find it no problem. sounds like this wiring harness is hooked up backwards or has a loose connection. also how did you test the alternator? the best way is to start vehicle and disconnect battery, Also what amps are you running at with vehicle running? Do you have any excessive car audio like a capictor or huge amp? Any squeaing from the belt might not be tight enough?
Battery is draining. 3rd battery - last one 6 months old. Diagnostics - starter, alternator, fanbelt all ok. Take the negative off terminal and battery starts charging itself. High Beam light is permanently on but not enough to be draining this way. Other problems - driver's lock wont work and passenger's window only works from driver side. Battery is main concern. Can't afford a mechanic checking a 1000 wires. Fuses ok too. Any ideas?