Could there be a rectifier problem in the alternator? If some of the diodes are not open-circuited, you'll lose charging capacity and you may get more 'pulsing' of rectified AC.

It might be in the voltage regulator, but I can't think of what would cause it to pulse.

Can you have a tech put a charging system tester on and let you know capacity, etc.?

My $0.02

BCingU, Jim