Did you have the alternator checked...? If not, how do you know the "alternator seems fine"? Not trying to get on your case, but faulty alternators look just like good ones....they just don't charge....and what were your symtoms again?
Seriously, check out that alternator. Sounds like you may have had a flakey voltage regulator because your red light went out when it was replaced. Now, we need to be sure your alternator doesn't have a broken field coil, or something else that's causing it not to produce a charge. A shop specializing in starters/alternators should be able to check it for you for little or nothing. But, you'll have to take it off and take it to them first.
If your alternator checks okay, and you know you've already replaced the voltage regulator, hell, the only thing left is wiring....maybe a bad ground wire, loose or intermittent contact, bad battery - maybe, but probably not. Faulty or intermittent ground wires would probably be in your ammeter circuit. I'd be willing to bet everything's okay with your alternator, voltage regulator, and battery, but your ammeter has fried it's guts....just a guess here.
Check out that alternator and let us know what turns up.
Anyone else got any more ideas....?