Probably didnt wire up your alternator right and you are melting the wires. Look over your circuitry again and make sure everything goes where it needs to go (no positive cables running to the negative, stuff like that).
There are two wires coming out of the altnator how do i know which one charges the battery and which one runs the headlights? Will one wire not be used since im not using headlights?
Yeah, you only need 1 wire if your not using your headlights. The charging wire goes to the same terminal on the solenoid as the battery connects to. You want that wire to basically go straight to the battery to charge it but normally the wire isn't long enough so the next best thing to do it connect it to the solenoid.
Where did you connect the wire to? Did you connect both wires? Where did you put the other wire?
You should not put the two stator wires together red wire is dc voltage for charging the battery white wire is ac voltage for the head lights . By hooking them together you could have dammaged the stator ,did you cut the plug off the stator