When you installed the aftermarket seat, I'll bet you raised the seating position by maybe an inch. With the same handlebar position you now lean slightly more forward. To keep your eyes level with the horizon you tilt your head ever-so-slightly back. That can cause stingers at the base of the neck. I have this problem when I ride any of Voni's bikes any distance at all. On my R1150R I had to install bar risers - up 1 inch, back 1/4 inch - to eliminate the issue.