So my warning lights came back on again today and now are staying on for longer periods of time. My plan is to replace the alternator with a re-manufactured Denso first, but I still think the symptoms favor an electrical short and not a failing alternator. The existing alternator is 4 years old and the 2 previous Advanced Auto alternators lasted 4 and 5 years, respectively. If after replacing the alternator I still get warning lights, which is what I expect, I'll start stripping the wiring harness and look into the relay behind the glove box.
If the new alternator solves the problem I'll take my old alternator back to AA and politely tell them they will no longer get any of my business.