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I recently got an ltr 2006 ran it for a while at the track after a lap the bike wud start cutting and bogging sort of misfiring but once I switch the bike of and on it runs fine. I opened the engine and replaced the complete bottom and top end did the clearances on the cylinder heads and everything was perfect jst to be sure also changed the fuel pump, water pump, oil pump and injector as well as the fuel filers but the bike is still doing the same. It's almost as of when the bike warms up it starts misfiring but as soon as I switch the bike on and off it's runs well again for about half a lap before starting to misfire again any suggestions I would be really grateful. I've also checked the fans and the wiring to the stator checked the stator and the regulator everything is fine. Any other suggestions???
 

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I would check the fuel pump, to be sure it isn't experiencing bleed-off. This sounds similar to what I was experiencing, and couldn't remedy, for the longest while. Ultimately after replacing everything you did, I bolstered the existing output seal(sort of triangular in shape)by forcing another round o-ring over top of it, and it finally remedied my issue. You can actually hear the pump prime now, and the bike won't shut off after running for a few seconds.
 
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