Rough Running

Backfiring from exhaust is running rich, from intake is lean.
But if you're revving hard at a standstill you need to bare in mind the fueling is designed that you'll be moving at those rpm ranges and it will be expectant on getting more air / intake pressure as a result.

As susggested a changed exhaust can cause problems if not remapped to account for it.

A vac leak will cause an erratic idle, you should also notice a greater than usual drop in revs when engaging gears and bringing the clutch to bite point without pulling away.

On an FI bike small differences will be ironed out by the ECU for you, and the air filter won't be in need of change for some time on a '10 bike unless you ride in London all day long
How many miles on it and what is the usage (communting, social, etc).

Has the battery been disconnected, bike dropped or such. If the TPS (throttle position sensor) is out of whack that could cause your idle / flat spot problems. A google search should identify a way to reset it, usually using key turns and buttons on the clocks or leaving the bike at idle for a period of time.