Also - check to see that your regulator is sensing voltage at the most remote point in your system. If you have the alternator / regulator sensing voltage at the battery, or somewhere close to the alternator output you'll never produce high enough voltage to power your cars electrical system and charge the battery at the same time.
When I re-wired my car, I routed the sensing wire for the internal regulator on my alternator directly from the fuse block. That way, I can make sure that I always have the correct voltage to power everything when the alternator is actually spinning. The closer you get to the alternator, the higher voltage you are going to have on the sensing wire - thus, the less the alternator thinks it has to put out. I'd definitely take readings on the sensing wire and see what type of voltage it's reading vs. the alternator output.