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We had a similar problem on a 97 or 98 sp 500. Going downa the road at full throttle it would stumble and run rough until we feathered the throttle a bit until it came out of it. When we looked at the boot between the air box and carb it was all wet. When we pulled the pre-cleaner off the air filter it ran better. I would sugest the a new air filter and the new type of pre-cleaner.
What do you have the fuel screw set at? Seems like you are getting to much fuel. Try turning it all the way in. Then back out 1 1/2 turn, to start. When you say it runs better without the air filter on, does it rev up properly? And does it bogg down around half throttle with air filter on? If so do you have a precleaner in the inlet of your air box? If not, with it running, grab your rubber intake boot on the air box and squeeze it closed about half way and then hit the throttle. Give it a try.
the only outside ajustment on the carb is the air screw/pilot screw ...it revs up fine without the filter but you cant even get half throttle with it on it doesnt look dirty at all its got to be the carb or something making it throw gas into the filter .....will try setting the air screw again
did you put the stock jetting back in the carb and set the c clip back in the right slot. make sure the air screw was set back at the right turns out. w/ the filter off it would run leaner as would a cracked carb. boot not richer. make sure the float level in the bowl is set level as well.
does it sound like it wants to back fire right through the air box, you may have a bad cam. do you run a lot of short trips? If so this will build condensation up inside the engine and when water is at the bottom of either the tank or crankcase it will be pumped right up to the highest point of engine thus wearing the big lobe on the camshaft(exhaust). When the lifter tries to go over the worn lobe it just spits back through intake. Just a possibility, Happy Hunting [img]i/expressions/face-icon-small-smile.gif[/img]