Since the Z is in the shop, I've started driving my 94 stealth. When I went to start it after sitting for a few months, battery was dead. No huge surprise there. So, I replace the battery; starts right up. I noticed when I drove it though, that the battery gauge would go up and down a little when I'd give it gas.

I drove it for about a week and a half without problem, then I let it sit in the garage for a few days, and when I went to start it, it was completely dead. Checked the batt voltage, it was less than 3v.

Bad alternator or something else?

 

If you have a voltmeter, then just check the current when the engine is running. If it hits 14 volts, your fine and the alternator is charging. If you don't get over twelve, then your running on the battery and the alt is screwed.
Will

 

Take it to Autozone or another parts store, they will check your charging system free of charge.

 

Get a large screwdriver and put the blade end on the front area of the alt. case. Put the handle end up against your ear. Do the same at the other end. If you hear a loud grinding noise, remove it and take it to an auto store for a bench test.
Oh, yeh, watch out for the drive belts when you do this. Jumping needle also is a good indication.