Regarding the vibration, most bike have a vib- RPM,,, either get above that rpm or below it, when cruising,,
and take some weight on your feet now and again to ease back & but pain on long hauls,,
2nd & 3rd,, Thats strange, have you checked the gear linkage for tightness & wear, . i had this problem on Sunday, after riding home from Blackpool. was hitting false neutrals, and had to double shift with foot to find gears, turns out the linkage was loose,,