Increase the idle speed a couple hundred rpms?
Is the Alt out put as good as it should be?
The AC tends to slow down the engine rpm, so bumping it up a bit may solve the problem.
Most high amp alternator still need to spin at a higher rpm to charge at full capacity, but maybe yours is not putting out as much as it should. I am assuming you upgraded the car wiring and the voltage regulator when you installed the 100 amp alt., if you didn't that is probably your problem. Gene