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Random limit at 2500-3000 rpm...sometimes

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2000 WR400. Has been running great for months.  Everything is stock except for the jets. I was riding one day on some trails here in Colorado. Day 1 I stopped the bike and took a break for 10 minutes. Started it back up and the bike had no power. It will take off with the clutch and 1500 rpm and then it just boggs out with throttle. If I full throttle it and hold, the bike just dies. It does backfire and is running super super lean and quickly overheats. I managed to limp back to the truck. 

Day 2 Pull the carb, and cleaned everything (new gaskets, new valves, seems to be working). Pulled the cap, adjusted the valves, checked the plug. Start it up. Same problem...boggs down to throttle response and then dies. It will idle just fine. 

Day 3 Pull the exhaust off and check the gasket (good), pull the petcock off (good), check the gas cap (good), Fuel line to carb(good). Start it up, same issue. 

Day 4 New boot between carb and engine intake. Check for leaks. Start it up same problem. Notice a slight oil leak at the bolt that holds the decompression lever. Pull the bolt out, add a new washer. Starts up and run perfect. 

Day 5 I ride like a madman for 5 hours straight and not a single problem. 

Day 6 Assume the bike is good. Head out to the trails things are great. Take a break for 2-3 minutes. Start it up...bogging down again with throttle. Sit for a few minutes, start it up and it runs fine for 3-4 hours. Take a break again, start it up...bogging down and I manage to limp back to the car. Get home, start it up and it runs like a champ

Ideas?

Seems the trend is that when it gets hot and I take a break it has the bog syndrome.

Some of mine...overheating is my first thought? But, is there an associated problem with the overheating?  

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I pulled apart the stator jack located on the top tube and checked the coil resistance. Everything was fine. Went back to double check the readings and found the secondary coil pickup was "open." I pulled off the stator cover to check continuity on the wire. Continuity good. Placed leads back on jack and kept an eye on the readings as I jiggled the wire down near the flywheel... loose wire connection at stator unit. I need to order a flywheel puller. You pointed me in the right direction @krannie. Will post more as I move along.

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The problem was the pink wire at the connection to the pin in the jack on the stator side. Hard wired the connection because the pin would not come out.
Symptoms were no spark above 3200 rpm on secondary pickup coil (o-scope verified this). Would not want to start after it had died when wide open throttle. Took 10-15 kicks to get it started again.
Problem solved. Starts first kick every time again and I can rev it to max rpm.

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Updated again for future trouble shooting. 

The problem showed up again after the wire was fixed. Ultimately, I replaced the CDI unit and it runs normal again. 

Conclusion, if you have a magneto/stator problem most likely it damaged the CDI. 

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