Harry, you should really consider 2 batteries. One to run the car itself and the other to run the electronic gizmos. Or you could just have to batteries hooked up in parallel so that if one battery craped out the other would keep the car running.
Also since u upgraded the alternator, i would seriously consider uprading the wiring as well. It could be one of the causes of the problem. Also what gauage wiring are u using for the electronics any way?