From my recent experience, the top two suspects for me would be the accessory plug on the alternator (3-wire connector) or the positive battery cable. Oh, make sure you've cleaned the ground connection wires, too. When I had Advance Auto test everything, they told us the same thing: both the new alt & the new battery were fine. Their test equipment simply isn't the right stuff to trace the problem down.
In my case, I replaced the connector first & still had all of my problems. Taking it to an automotive electrical specialist (in this case, an R/V retrofit guy) gave me a way to test the entire system ($80). This provided him the info to determine that the positive cable had enough broken strands that it was killing both the alternator & the battery. He cut off the old terminal clamp & soldered on a new one.
All of our electrical problems were finally solved with that fix. If you don't want to keep guessing, find somebody with the proper test equipment.
"Help, Mr. Wiza-a-ard!!"