01 HPDI 200 Weird Issue

[DSires]

I've been having some weird issues with my motor, it started off as a bad coil pack that I have since changed, but I am still getting random symptoms of a bad coil pack. The problem seems to only occur after the motor warms up, yesterday I made about a 10 mile run with no issues, shut off the motor for about 20 mins to fish, then when I went to crank the motor back up it was running rough, same symptom of when I had bad coil pack or if it was a cylinder not firing. All I did was turn it off and turn it back on and it ran fine with no issues the rest of the day. I'm assuming this is some sort of electrical issue, is it possibly the wire harness? I have two connectors that plug into my coil packs that are suspect, one has been nicked from putting the motor cover back on, a little of the insulation has been removed and the wire was exposed, it has since been tapped up. I have another coil pack plug on the harness that has a broken clip, so it doesn't snap into the coil pack plug. That has been fixed with a zip tie that seems to be holding it securely. I would like to get a used wire harness and re splice some new connectors. Could either of these be causing me issues or is there anything else that I should look into?

[DSires]

Problem solved, it was a throttle position sensor that wasn't making contact in neutral anymore. The boat was constantly thinking it was in neutral so it was only running on 4 cylinders.