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More than likely bad fuel. Drain it & give it to someone you don't like. Put in fresh fuel and check your air cleaner. My old carb bike did the same thing every spring for the first tank or two of new fuel even with Fuel Stabilizer in it. My 07 FI doesn't seem as badly affected though. Fuel filter is supposed to be good for 50,000 but you know the quality of fuel in your area. Then again, What do I know? I'm not a certified MoCo technician.
as for the fuel issue, try putting just a little sea foam in your tank and riding through it.
The power issue to me actually sounds like a flooding issue, although strange on an injection engine. Change your oil and look at the consisancy of the fluid if it has gas in it you may have a larger problem. Most bikes loose compression and backfire when slightly flooded.
I would have the clutch investigated as well, but you can change your filters and oil at home and its a good thing to do regularly anyways.
Sounds to me like you have a intake leak, those exact symptoms effected my buddy last year, bike would run fine, then once warmed up would not go past 55. We initially thought fuel filter, but ended up pulling the intake and lo and behold the evidence was plain as day. Something to consider! Of course you can take what this back yard mechanic says with a grain of salt if you wish
I read somewhere that the problem might be the plug for the fuel injection...something about it not making a good connection and causing the slider to not open all the way..anyway pull the plug apart and look for corrosion clean it and add some dialectic grease
I'll take the backyard mechanic route any day. Thanks for all the help. If the f-in weather ever gets cleared up out here I'll take the bike out, clear up the problem and get ridin' again.
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