Did the alternator problem just appear through normal use or are you putting the car back together?
Does it happen while the car is stopped or only when the alternator is charging?
Have you got the cable connected to the correct terminals on the alternator and battery, I know it sounds stupid but worth checking as some alternators have a terminal on the back for an earth strap.
Are you getting power on the voltage "sense" wire from the Alt dash light at her alternator?
What amps and volts is the alternator putting out?
I would suspect you have an alternator issue such as an internal short of faulty internal regulator.