In the first pic, the mounting of the shifter kit is wrong. Where you have the studs, they shoudl go in holes just above that one, and it looks like you are missing a required spacer that definately comes with the kit, is an aluminum spacer that do in between the engine and shifter kit.
also, With the shifter kit comes bolts to replace the original mounting studs. to remove the studs. take two nuts and tighten them against each other, then put a wrench to the bottom nut, lefty loosey, righty tighty.
Of course i am assuming you purchased the Sick Bike Parts shifter kit and not the copy thats floating around the nets.
Here is the instructions form SBP http://www.sickbikeparts.com/Manuals...%20Rev%20A.pdf
iLook at all the parts in your kit you will see what im talking about.