Super Jet Chasing a issue -- Help me out

[IS0LD0UT]

Chasing an issue for some time and have not been able to find the source. Help me narrow down the things to try.

Back info
JM 735 with a b-pipe, stock ignition, stock 38s, SJ hull. The setup ran perfect all season, no changes made before the issue occurred. Fresh water only. Coupler cover is in place.

Symptoms / Issues
The engine started bogging hard from low throttle to 3/4, after a long freeride weekend and some double-up action. I thought I got water in the fuel or carb, or that is what it felt like. Or maybe running rich, or one one cylinder. If I pin the throttle the ski will eventually revup and take off with full power. I can also ride and keep the revs up higher and not see any issues. There was no milky stuff in the motor or plugs, so I don't think it was water ingestion.

After the freeride, the ski worked fine and then the issue showed up again after some hard riding. It did that a few times, running good the whole session, then running like crap a few times. Now it seems to run like crap more than good.
Engine starts and idles perfect.

What I have tried

1. Drained fuel
2. Tank holds pressure
3. Found small leak on carb back cover, replaced cover and gasket. Leak is fixed, still issues. Checked both carbs multiple times. They pop evenly and hold pressure. 50ish popoff.
4. Replaced fuel filter and one-way valve.
5. Checked fuel lines multiple times.
6. Plugs look good, brown. Turned the lows out more and it acted richer, turn them in and it ran lean.
7. Pulled the ebox, no water inside, stator wires tested out perfect.
8. Synced carbs with a snail meter.
9. Tested resistance through plug wires, it did not vary any when I flexed them. Although they are original wires.
10. Last time I was out I zip-tied the plug caps in place. This seemed to help quite a bit, so I replaced the plugs caps with msd. Yesterday, it was running perfect with the new caps till about 1/2 hour into the ride. I was doing some power subs and such when it started breaking up so maybe this is my clue. The remaining 1/2 hour it still was having the issue.

Current Thoughts
I am starting to think when it gets wet the issues show up. I had the ski in the garage for about 2 weeks this last time, plenty of time for things to dry out. As I wrote above yesterday the first 30 mins were perfect.

The stator I am using had the wires cut and they are held together with the epoxy sealing butt connectors.
Also my start stop connectors are at the bottom of the hull, water washing over them quite a bit.
When I tested them the ski was in the 2 week drying period mentioned. Would a little fresh water in a connector change the resistance enough to cause a spark issue?
This may explain why the issue comes and goes.

Also could the needle and seat be randomly sticking open? I had JM put new needles and seats in this year. It it poping fine when I pull the carbs around 55psi.

Things I was thinking of trying.

1. Change out coil, wires or coil are shot.
2. Cut and reconnect stator wires.
3. Different stator.
4. Timing, could that have moved? It starts fine and runs great sometimes, kinda hard to believe it would be moving around and still starting and running fine sometimes.
5. Needle and seat sticking randomly, how do you figure that out?

Let me know if you think I missed something, or an order of things to try.

 

[Crab]

lower your popoff , they can stick if there is any groove in the needle. I would go 40-45

 

[JetManiac]

Things I was thinking of trying.

1. Change out coil, wires or coil are shot. Replace with JSS coil, good idea anyway!
2. Cut and reconnect stator wires. Easy to try.
3. Different stator. Possible your charge coil is going bad, often they run good until they get hot, then all kinds of weird issues.
4. Timing, could that have moved? It starts fine and runs great sometimes, kinda hard to believe it would be moving around and still starting and running fine sometimes.
5. Needle and seat sticking randomly, how do you figure that out? Unlikely with new N&S already installed