I suspect that there is a fuse/circuit breaker blown. However, Reading over your comment a couple times, how did you know the wires were bare and shorted in the middle of the boat? Can you actually see those wires? And if so then I think only a fuse or circuit breaker is your problem. Your trolling motor would have not been effect because the short was before any of the current or voltage actually even made it to the trolling motor circuit. But make sure you rewire those wires and not just splice. Splicing wires will work short time but they will rear their ugly heads down the road... JMHO!