What should my idle voltage be?

That might be right for the stock 2G alternator. The engine should be running fine even if the alternator wasn't charging correctly.

If you do a 3G upgrade, I've read that they keep on pumping out 14v even with lights & air on.

What's your idle set at? Autos in a Drive gear tend to idle lower than many manual-transmission cars.

FWIW, 12.6 volts is break-even. If you are a hair under that while idling with some accessories on and as soon as the revs come up, the volts come up, you're doing just fine.

A 2G can dip into the low 11's at a loaded idle.

I'd look elsewhere for the missing. Pulling codes is the place to start. See Jrichker's 'dump the codes' post for info on doing so.

Good luck.