you have one of thee problems either short in alternator bad regulator IE not shutting off or bad starter solenoid . you did not say if you replaced wiring harness trying to fix problem or if it started after you replaced it , remove pos battery clamp put meter from clamp to battery unless you have an assecory like stereo with clock or memory it should show zero disconnect regulator if it shows 12 volts and see if it drops to 0 if it doesn't replace it some time people have swapped out alt. with external regulator and put in one with internal regulator with out changing some wiring this will cause things to get hot

I would suggest that one or both of the diode sets in the alternator is shorted.