Not as much fun.

I also had the same symptoms and the reason was the primary TPS. Replaced it and got the voltage right -> no more backfire or hiccups. With the broken TPS the bike was running really bad.
 

We just worked on a 2005 R3 & the problem we had was that it was sucking in air from the mounting boot on the intake stakes against the block. Since we didn't have spares we changed bolts and install it with ( Grey Gasket Make Grey ) to make sure it seal perfectly and this did the trick.Make sure you use minimal amount so that it does not go into the intake passages. This did the trip.