it almost seems like what happened to mine when flipped it. i had to replace my primary cover. every thing was good to go. when i went to shift it wouldnt. took every thing back off, nothing broke or missing. it seems that the shifter shaft was tweeked a bit. so i honed out the brass bushing. not to much. i was able to shift but some times i would have to move it back to center with my toe while shifting. now i dont because the bushing is now worn in. which is what has happend to you while riding about 06buelly.
0feedback if every thing in the primary is fine, i.g. the springs, shift forks, ect., try honing the brass bushing a bit. to make your own hone, get some emery cloth and a bolt that is a smaller dia. that the shift shaft. cut the head off the bolt, then make a cut in the center of the bolt as if you were going to split the bolt in half, but just about half inch down. place cloth in the slit you just make and wrap it around the bolt. place the bolt in a drill and slowly hone the bushing. or just go buy a small brake hone.