As Warp looks his first thought was for a 06 who and whats been done to the clutch. Or is the one of the first clutches fit on a 04 installed on a 06 to keep production line rolling.
Not know the answer I copied a couple pictures from this thread.
Firts the bike in question. I have never seen a lifter shaft with no center hole and no visible splines and center hole for manufacturing showing. Like in the third picture
This makes me wonder who has been in this motor trying work on the clutch.
Another thought that popped in my mind is if they were in it did they stack the clutch right or is on of the smaller Inside diameter fibers interfering with the anti shudder spring and seat. Then well it also sounds like some of the steels are warped and kind of grabbing as she warms up. With the clutch kind of grabbing and rotating the input shaft a we bit could make it hard to select gears and shift.
I'd spend the few hours and open her up for inspection.
In my opinion this should be done verses all the trial and error testing that could be hurting something in the gear box.
Sorry it took so long for me to notice this thread.