So I have an issue apparently with my wiring harness. The boat shop has told me there is a short somewhere in my wiring harness and that is the reason it will not turn over. They are quoting me $2000 to install a new wiring harness and that may/may not fix it. So am I getting raked over the coals or is this ligit? Are they not wanting to take the time to just find the places where a short may be? I'm kind of at a loss right now. Thanks in advance for the responses.

Take it to another shop. If for instance the neutral safety switch wire is open, run a new individual wire. When you have a short the circuit will blow the fuse. When you have an open circuit you have nothing. Each wire that is suspect can be tested with an ohm meter. It is very possible you have a corroded plug connector between the control and the ignition switch. Seen several boats that have been around salt water have these issues. Just looked and both types of controls have plug connectors for the neutral safety switch and all other wiring.

TAKE YOUR BOAT/ENGINE SOMEWHERE ELSE!
No need to replace a whole harness for a "possible" short! That is a I don't know what he11 I'm doing fix! What is the issue it's having?

Yup thanks guys. That's what I thought. I hate not knowing how to fix and test things. The issue I took it in for was that after running it all day I was idling back in to the dock and it just stopped. It will crank fine but it will just not turn over. I thought it would be an easy fix...ignition seems fine and I think it is firing, but it seems to not get any gas. I thought maybe the vft was clogged or a sensor issue to the low pressure fuel pump. He did state that when he wiggled the wires the fuel pump worked. I'm going to get a second opinion for sure.

crank fine but it will just not turn over. For your information cranking and turning over are the same thing.

What I meant by that the batteries are strong but it will not start. So, the motor will just sit there and not act like it will try to start like the kill switch is not in.