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2000 Johnson 200 OceanPro J200VXSSS intermittent issue

Show up to the dock 4:30 am pump bulb choke and start engine she stumbles once I choke and start again she runs in idle everything like usual for a 2 cycle kinda used to that start. Idle is fine warm up 20 mins pisser is good and we head out to the spot. After a 45 minute run at 3800-4200 RPM we let the engine run in idle for 5 mins prior to shut down to start some fishing, the entire time there was no stumble, no miss, no fart, no sneeze, no cough, everything as I would expect out of the outboard including no excessive smoke at idle or run. Fished a drift for about 30-45 mins and at next start up the engine idled rough stumbled, a fart and cough out of the exhaust, had to restart 3 times, had to advance the throttle a little to keep it running to prevent it dropping out. After running the engine a little bit with the poor start it will run normal again even idle correctly. Engine has 430 hours fuel is treated with startron every fill, engine fogged every fall, compression is 95-100 all cylinders, XD50 2 cycle oil since I have owned it, new separator and fuel filters this spring, also tested on a remote tank and it did the same, VRO replaced last year, new plugs and checked gap before install in spring, passes 7/16 gap spark test, fuel bulb form and replaced last season. This intermittent problem is happening more often this season but it occured less than a handful of times last season.

For others who have had this similar failure what was the solution for this intermittent problem even if you could point out what particular devices were the root cause failure I will test the device along side the instructions of my Johnson Evinrude service manual.
 
Yes all six bowls are plastic but if your referring to the bowl allowing additional air to leak into the bowl how come when I slightly advance the throttle during an instance when my intermittent issue occurs, the cough and hard idle goes away, wouldn't it act up more often if the bowls were the issue? It only acts up after a long run out to my fishing spots after turning the engine off than back on it gives me a hiccup? Warped bowls should be a problem all the time should it not? And like I said after the problem resurfaces, if I just run the engine with advanced throttle for a short bit the problem seems to weasel it self out? So awkward honestly i wish some thing would just flat out break so i can replace it....lol

Side note, motor runs excellent through entire RPM range quickstart begins than it backs off after warm nuetral idle at 750 RPM when it doesn't hiccup that is and in gear 650 RPM

Sometimes after a hard run like 5200 RPM and back off to idle, the idle is pure poop like rough and stumble....this happens sometimes to so I cleaned the low speed carb circuits and idle air mixture valves and that didn't help but it did make my idle when the engine is running properly more stable and less rough
 
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Having retired in 1991, I'm sort of stumbling into forbidden territory here as I have no idea of the ignition design of the 2000 model V6. However, if the ignition is the Capacitance Discharge Ignition with a stator under the flywheel, the stator would be the beginning of both the ignition and battery charging system... and at the rear portion of that stator would be two large black coils that provide approximately 300v AC to the powerpack capacitor.

Those stators run extremely hot and eventually those black coils (at least one of them) encounter a melt-down point whereas a sticky looking substance begins to drip down on the powerhead area. This results in weak, erratic, and eventually no ignition... plus other strange happenings while the stator is going through its failing stages. Observe the stator if it exists, and if a "meltdown" scenario does exist, replace the stator regardless of what reading you may obtain from it.

This may or may not pertain to your 2000 V6... BUT... knowing the situation does exist can't hurt.
 
Yes the goeey substance you speak about is present on my stator and I have measured the resistance of the coils at standstill cold when I recently replaced my regulator/rectifier because its output was too high and it was 18 years old....lol...it had finally failed after 18 years.....the stator is a hard to find parts for my V6 at the cost of 350-400 but I could see after a heat soak that it may possible be failing and after the flywheel begins to turn again it cools the coil again and works ok till the next heat soak......I have thought about this as well but the resistance reading for the ignition coils on the stator seemed ok at cold and the charge coils were ok which I verified when I replaced the reg/rectifier in the spring so it had me thinking the stator may be ok but not so after a heat soak......I may just take the dive and buy the stator pull the flywheel and inspect the magnets and timer base at the same time for any anomalies, any chance you think the timer base could be intermittent?
 
here is a diagram of the parts of the ignition system im pretty sure since it seems you have worked on outboards before you could just tell by the diagram what kind of ignition system it is.....
 

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