I took it for a ride today and when i got back i noticed a little box that is mounted on the outside of the frame right above the rear foot peg on the right side of the bike (if you are sitting on it). It started smoking and got really hot. Just wondering what that controls and what to do to fix it?

 

Could you be talking about the regulator/rectifier? If thats what you're talking about it does two things. It changes the AC from your stator to DC since everything on the bike runs off DC. It also regulates the voltage so you only get your 13-14 volts to keep your battery fresh. I used to have an F2 and then a 95 900RR. I never had any trouble with the 900, but the F2 went through 2 regulator/rectifiers. A weak battery can cause one to burn up as well as trying to jumpstart the bike from a car battery. After the 2nd one on the F2, i rigged up a small fan to keep mine cool and I never went through another one again.