I would replace the wireing in the boat for sure. But first I would unplug the control at the motor big plug and start the motor with a starter and see if it still shorts out or I would pull every wire loose one at a time and see which one shorted out. The starter isn't the one doing it to you there is something sending power back to the starter while the motor is running.

 

so theres probably something in the control box/cables and ignition switch thats screwing the starter up

 

so theres probably something in the control box/cables and ignition switch thats screwing the starter up

If I was a guessing man I would suspect it to be so.

 

how hard is it to replace all the wiring and should i do it myself or have someone else do it to keep from doing something wrong and frying everything

 

the control box on an outboard is completly isolated from the boat that it is mounted to, meaning that the control box can be completly removed from the boat and the motor will still run , the only exception is that it gets its power from the two large batery cables at the bateries, and thats it, I'll bet anything that their is NO connection to the boats wirring problem and the control box for the outboard.