This is for an 06 R6 but the principle is the same for any bike with a similar shift setup that has tight frame clearances around the rod/tranny connection.
A little hint that matches my preferences. After you switch over to GP shift, with the stock linkage, you will notice that the shift rod needs a LOT of adjustment to get back to the same position it was in. In addition to that, I like to adjust the pedal further to put it up fairly high. This makes it easy to get my foot underneath it, as well as making it easy to click off a clutchless upshift while hanging off the right side of the bike.
To get the pedal high, I just adjusted the shifter so that when it is pressed all the way down, i.e. it's farthest point during a shift, the knob JUST clears the frame.
Like this:
Nicely adjusted:
