Well there you have it, now you know what wires to trace down. I would take an ohm metter with you so you can test the wires all the way through to the ECU.

Dustin, i am the guy doing the work to the this boat and will check the wires in the morning. Are the wires in the factory harness or the whipple harness and what am i testing for. power ?, 5.0 volts ? , ohms ? The whipple check engine light will also go out when the boat is in timing mode which makes me believe that the harness is okay. Thanks for your help !!!