when my last alternator went out, it would take 3 days to discharge the battery far enough to either not start or stall. the headlights would dim, the dash lights would dim, then just before it went out, the tranny would not shift properly and then shut the engine off. i would charge the battery and it would take 3 days to do it again. swapped the alternator for a used one and never had that problem again.
so, i don't know, different experiences, i guess.
I agree that can happen, I have seen this kind of problem too, in my case the alternator still worked but not at 100% capacity, it was putting out some power but not enough to keep the battery charged, so after a while the battery would get low enough that the engine wouldn't start. An alternator doesn't always just flat die, sometimes it can be dying but still put out some power, just not quite enough power, so the car is using a little bit of battery power to keep running.
Although I have also seen really similar behavior when the battery was no good.
At any rate, I don't see how we can help you much other than with generic advice, what you need to be doing is troubleshooting the issue one thing at a time, charging system issues are usually really simple, you can just check your cables, grounds, and connection points, remove the battery and test it by itself, remove the alternator and test it by itself... There's only a few things that could go wrong, you should find the issue easy enough. If you have Autozone nearby they will test these parts for free. They can test them on the vehicle but those tests don't always prove conclusive.
Since you were working in the area of the valve covers that makes me more inclined to think you might have loosened the ground strap or left it disconnected or something, that or some other wire. Once again this is only a guess though without being there to look things over <img src="/forums/images/graemlins/smile.gif" alt="" />
