Ok, sounds good. That's on my list this weekend. I'll run 8 gauge just to be safe. If I get bored, I'll rewrap the harness to give it a nice clean factory look.
So after doing this, I'll run the engine a while to get the battery topped off then check the voltage at the alternator and the battery. If I understand correctly, it should be almost the same since there is now so little resistance.
I'm always a little paranoid of electrical stuff, probably because I understand it the least of all my cars workings. I plan to keep checking it regularly too in case the alternator is acting up.
Thanks for all the great advice.