You didn't mention the air filter - did you replace or clean it?
Make sure there's nothing under the seat blocking the intake to the airbox.
You could pull the plugs and take a look for clues. You can also check the exhaust pipes with an IR thermometer to see if both cylinders are firing and running the same.
How well does it crank over? A dead battery can cause it to run poorly. Check to see that you have at least 12.7V before turning anything on.
How old is the gas? Bad gas or gas with water (condensation) can cause what you described. If there's any question, I'd completely drain the tank and floatbowls.
Don't bother revving when not under load (riding). The requirements (ignition, air, carb jetting, fuel quality) to rev freely are way less than what is required under load and it doesn't really tell you anything when troubleshooting.
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