650sx complete rebuild, new electrics, won't run

Need some thoughts. Went through this ski & engine, did a new top end (bore and new pistons), leak down tested, rebuilt carb, swapped out stator for known good one, rebuilt CDI by JSS, put a known working regulator/rectifier in and the ski still having issues.

Put it in the water and it runs great for 10 - 15 minutes typically. Sometimes 30 + minutes, sometimes 2 -3 minutes before it bogs and dies. If I am lucky it will idle and I can limp back to dock, let it sit for 15 - 20 minutes and it's back to doing the same exact thing.

Thoughts are it has to be electrical. Start / stop switch possible ? Ground getting hot ? Thoughts appreciated. No idea where to go next.
 

bored&stroked

Urban redneck
Location
AZ
My buddy went threw something just like this, ended up being spark plug caps!!!!!!! Only took him over a year and every single electrical part new from yamaha on his superjet to figure it out.
 
Need some thoughts. Went through this ski & engine, did a new top end (bore and new pistons), leak down tested, rebuilt carb, swapped out stator for known good one, rebuilt CDI by JSS, put a known working regulator/rectifier in and the ski still having issues.

Put it in the water and it runs great for 10 - 15 minutes typically. Sometimes 30 + minutes, sometimes 2 -3 minutes before it bogs and dies. If I am lucky it will idle and I can limp back to dock, let it sit for 15 - 20 minutes and it's back to doing the same exact thing.

Thoughts are it has to be electrical. Start / stop switch possible ? Ground getting hot ? Thoughts appreciated. No idea where to go next.

I have exactly the same problem
I had my crank rebuilt ran fine for first outing, next time 1 hour or so and then cut out and will start and idle any throttle and cuts out
So I fitted a used Cdi and the same problem
So bought a new igniter coil from wsm it didn't work no spark whatsoever ever
So I had the original coil rewound, replaced all the wiring all the way to the cdi sorrted ran fine for 3 outings of 2 hours or so non stop use then today just on last blast it stopped idling then back to the same problem again
The ignition is so simple flywheel rotates as it passes the igniter coil which generates the spark the current goes the the Cdi coil
then Cdi the to the plugs which both fire at the same time

So how can it be so difficult a problem

Onether thing was I replaced the flywheel I'm wondering if the magnets have lost their. Magnetium
Cheers mark
 
If you need a new stator or ebox I have both. I'm not sure that it could even be this but if you have an exhaust leak it will run like crap, I kept blowing off my silicone coupler and it will not run past half throttle. You would be able to notice smoke in the boat when you stop quickly and pull the hod off. I saw that someone above said something about the spark plug caps coming off, I also had this issue but it caused more of a miss. I ended up buying solid terminal BR7ES spark plugs to keep this from happening.
 
Location
V-town
i had a similar issue with a failing head gasket.... replaced every electrical part and nothing fixed it. pulled the engine and head realized the deck wasn't 100% flat. seemed like it only did it after about 10-15 minutes... would cool down and seal I dont know but every time i would pull plugs check for spark, et it sit and then good to go for 15 minutes after 30ish minutes of sitting.
 
Location
V-town
i did and thats why i never thought head gasket... compression was around 180 when it would break down and a little lower after sitting in the garage for a few days.
i literally changed ebox, stator, flywheel, start stop switch, a new tested good coil, a known good coil, a known good regulator numerous plugs.... the plugs never looked bad either. no water on them I was 100% positive it was electrical- for months i battled it. until i removed the engine to run another. I sorta recall doing a leak down test once the motor was out but it didn't give me the ahhh haaa!!! upon teardown i thought it was a base gasket- until i had a straight edge on the jugs... a cylinder had dropped a tiny bit.
 
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