Sounds like a bad solder joint. Everytime I've had motor wires get hot it was a poor solder joint on one of the bullets. Crappy solder joint = higher resistance = heat.... I'd check that out first.

Technically it's not the best system for 3s, but I've gotten away with it before, especially in a light 2wd like a Rustler. However 3s in a 4wd SCT is a definite no go.