Hello today I was disassembling my alternator to send the housing off to get polished and I had to use a vice with a towel on it just to get the top bolt off for the pulley. It seems like it took a little bit of metal off, and it kinda looks like scoring or scuffs on the rotor. Will this affect anything as I know nothing about electrical.

 

Nope, won't hurt it at all. If there are any raised burrs that grab your skin you want to sand them down by hand with some sandpaper though. Alternators take a beating because they have so many openings around them.