in any gear if i am under 3500 RPM my 1000rr sputters bad i had that infamous stator problem replaced the stator, flywheel, and regulater/rectifier
it sat for about 2 months ant ideas before i start wrenchen

 

Could be a number of things really, but since its been sitting, could be crap formed in your tank, bad fuel (it does go off) check your in line filter for debris.

 

Oh,1 more thing, you can get condensation (water) forming in your tank, that just runs down and sits in the tank as well, does not mix well with fuel. (even if your bike ain't being used) specially if there have been big differences in ambient temps. used to happen with my K100 beemer, cos the tank would get so hot, so when it cooled, formed condensation. Check your plugs and so on as well.