My lights are very dim and the starter cranks over sluggishly, so i checked out the alternator and noticed that the output wire is schorched and the boot that covers it is charred. I have the stock ext. regulated alternator. I am now considering going to a cs130 or 144 one wire system. Should i be worried about it being something else causing the hot wires?

Maybe some other opinions. Unless you have an idea when it happened, it's only a guess. Normally burnt wires occur near the shorted area and burn away from the short. A guess would be that there was an alternator problem at one time. Perhaps the alternator was changed out after the burn ocurred.