Think the problem is in the Rube Goldberg shifting mechanism which is not aligned with the center axis of the bike. In another thread (Shifting Technique or pre-loading the shifter) I detailed going with a Continental shifter on the Interceptor. There are way too many moving parts in the shifting mechanism from the factory. The Conti shifter comes directly off the transmission spline and works great on the Interceptor. Removing all that hardware, foot rest and all, I moved the passenger foot peg down to the lower hole (after running a tap to clean the threads) and locked it in with a nut.
This lowers the peg and moves it to the rear a bit. At 900 miles +, shifting is positive and very smooth.
I wouldn't fool with the stock shifter and expect much from it, too much free play with the turnbuckles and angles. I played with mine quite a bit before going with a Conti shifter, about $31 USD from the dealer.
Good Luck.