Take the fuse block off and look at the back of it. It should be jumpered from the main supply off to all the other sources, such as accessory plugs, lights, ign, etc. If this jumper is loose or corroded, it could be giving you a bad connection.
If you have a shorted voltage reg, you would get no regulation at all, so your lights should be very bright and pulsing with the motor. If you know for sure, I would replace it before you damage the CDI or something else. First, get a meter and check the regulator according to the manuals' instructions. Check grounds, and output from the regulator. If you're getting 18+Volts out of it, the regulator is gone, it should charge about 14-14.5Vdc at idle or justa above. Just go across the battery to measure this.
Lastly, go over the wiring harness carefully and look for anything that may be pinched, damaged insulation.
Mine: '03 400 manual, ACT,27" Bearclaws, Warn, LED's <div align="center">[/center]
Hers: '04 400 Auto, FIS, 25" Goodyears, Champion 3000#, lights, bumpers[center]</div>