So had to update. I FUCKING FIXED IT. What a long summer last year chasing this issue. Had to run it 3 times this summer just to confirm I actually ACTUALLY fixed it.
It was the IGNITION COIL. Big thanks to roosm. I guess it must overheat after an hour of use.
So here is a final list of things I replaced/addressed trying to track down this issue. Got a lot of 'long term' maintenance items knocked out cuz of this issue. Should add, I don't think the boat threw any codes this entire time that weren't my own doing by unplugging wires, etc. I don't think it was ever going in to limp mode.
1) Spark plugs
2) Plug wires
3) Distributor Cap
4) Throttle Position Sensor (left old one in, because new one cause it to run extremely rich/rough)
5) Fuel Filter
6) Both Fuel Lines (found a leaky line which made this entire endeavor worth it)
7) Impeller
8 ) Transmission Cooler Inspect/Clear
9) Fuel pick up tube
10) Ignition Coil
On another note. I was losing power and getting symptoms of running out of gas this past weekend despite having a half tank. I had felt minor symptoms over the past month, but chalked it up to prop wash. Then on the trailer it wouldn't even start and the fuel pump wasn't priming or making noise. I replaced the fuel pump ($400 part!) and it still didn't make noise. No 12v to the pump wires either. I traced the power lines to some in line fuses, and bam one was shot. Plugged a new one in and it ran perfectly tonight. A full 30 psi from the fuel rail. I think the fuel pump died and threw a fuse on the way out.
Oh yeah and that short on the wake plate was because the wires running from the steering column to the stern were rubbing on the sharp edge of the aftermarket radio and grounded them out.
What a trip these boats can be. Hoping I can make it the rest of the summer without another issue!