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07 MXZ XRS 800 Acting up! Help??

I have a 07 XRS that I bought new and never had any trouble until this year. I have a problem and cannot figure out what is wrong with it.Let me start from the begining so you know the history I went 70 miles at the begining of the season and lost the compression in the PTO side cylinder. I found that the Ring Pin had broke and the ring spun around on the piston and when it finnaly got to the exhaust port it opened up enough to break the ring and ruin the cylinder. I replaced the cylinder and both pistons. This ran like a top for about 100 miles after the engine overhaul. Now when you start it will run excellent for about 5 -10 miles and then it acts just like you are turning the kill switch on and off with no beeps or engine warning lights. It will sit and idle geat, but if you give it throttle it will cut out and if you give it full throttle it will completly kill the engine. It will cut out to one cylinder and then it will come back into it and run great again for an unknown amout of time, then it will start cutting out again. I can't figure out if it is a fire or fuel problem. I checked all my wires. I have unplugged the wires to the kill switch and ran it. I have check all the fuel lines. I have added that K100 to the fuel ( due to our gas now has Ethenol in it ) I've loosend up the fuel cap when it starts to act up thinkin that maybe a vent was plugged. I have replaced both plugs and plug wires and caps. I can't link the problem to anything. Like I said, it will run perfect if you let it set with the engine off for a while. This leaves me to believe it has to do with the temp of the engine or a fuel restriction somewhere. Sensor? Any help or direction would be greatly appricated. This is driving me nuts to figure out what is wrong!
Thanks
 
Here are a few things to check: first, make the problem happen; remove spark plugs, are they wet, dry, white, or black? Just one side? After you have determined which cylinder is cutting out, try draining that cyl's float bowl, if nothing comes out of the carb, then you know you have a fuel delivery problem.

Had one do exactly what you were talking about and it ended up being a piece of red paint (the color of our fuel caddy) that was intermittently stopping the fuel flow to one cylinder at a time, if you would let it sit, it would start back up and run on both cylinders for a short while.

Next, purchase an inline spark tester, make the problem happen and determine if it is spark related. If it is, check the ECM connection for any green corrosion on the ECM pins and the main wiring harness plug.

Check the wires from the TPS on the carbs, they have been known to rub through on places they shouldn't.

Check the handlebar wiring harness under the tach/speedo, make sure to apply di-electric grease to the connections. Again, check for any corrosion on the terminals.

If none of these help, bring it into a dealer and check for any weird faults.

Hope this helps.
 
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