Here's what I know about electrical problems... I HATE them! But beyond that I try to keep my troubleshooting simple (because I'm not an engineer or particularly technical) so here's the best I can do for you (I have yet to troubleshoot electrical issues on my y2k, hopefully attempting to help w/ a '99 is as close as I get):
The voltage regulator is electronic (EVR)... it is located w/in the PCM... if the regulator is bad the PCM must be replaced (per the DC service manual). The only option here might be checking for a trouble code. (DTC). PCM is covered by the emissions warranty to 80k miles...
Here are the basics of how an alternator works (as I understand it)... 1) engine runs, pulley spins and at sufficient rpm (for a y2k idle is sufficient rpm), 2) voltage regulator does something and electrical power is supplied to the alternator energizing the magnets, 3) power is generated. With this understanding check to see if the field wires (2 small wires on the back of the alternator are field wires, the one large wire directs any resulting charge to the battery) are supplying power to the alternator (use a simple light tester or a volt meter). Possible problems:
If there is no power at the alternator the magnets are not being energized, thus no power is generated. This could be a bad fuse (check relevant fuses in the fuseblock in the cab and power distribution center under the hood). If it is not a fuse then it really suggests the voltage regulator (EVR)/PCM.
If there is field power at the alternator sounds like a bad alternator (easiest test is to pull it and take it to an Autozone or any place else that will do a free test).
Hope this helps... I'd be interested in hearing how it works out... and if the above was useful/useless.
HAPPY NEW YEAR!!!!
jm