The first 'nub' we encountered was August of 2006 at the Redding Tech Daze (great function). EagleMike, TOBJ, Larryboy, MotoPhoto, and other knowledgeable KLRistas. They could not get the valve cover off the 2007 KLR650. They ended up using a dremel to remove the valve cover. After it was off they ground it smooth and painted the valve cover. If you did not know, you wouldn't.
So if you...
...remove the gasket.
...lift the valve cover at an angle.
...use a light loose wiggle hand so the valve cover does not bind.
...stop and start.
...then you need to trim some of the nub off to remove the valve cover.
...after the valve cover is removed you can do what you need to do to make you happy.
Hope this helps.
TIP: after you change the valve shims and have everything, except the valve cover, rotate the engine at least two times, by hand, and recheck the clearances.
2005 KLR 685
2015 Yamaha Super Tenere ES, 5/23/2015
2012 Yamaha Super Tenere; Purchased 7/30/2011; Sold 5/23/2015