I feel you, I wear a similar size (10) boot and it was a learning curve for me to shift on this bike. I catch the shifter with the top side of my boot sole, been shifting like that for years as I found it diffcult to get my toe under most shifters.
I found this on the forum:
http://www.r3-forums.com/forum/522-drivetrain/4601-adjusting-shifter-r3.html
here is a youtube video showing how to adjust the shifter, different bike but similar idea:
https://www.youtube.com/watch?v=5ulz5vLCoKQ
it would appear that he shifter is adjustable, maybe give this a try it.
Most of the rear sets I have seen for the r3 put the Peg and the Shifter in a more aggressive riding position.
I found this on the forum:
http://www.r3-forums.com/forum/522-drivetrain/4601-adjusting-shifter-r3.html
here is a youtube video showing how to adjust the shifter, different bike but similar idea:
https://www.youtube.com/watch?v=5ulz5vLCoKQ
it would appear that he shifter is adjustable, maybe give this a try it.
Most of the rear sets I have seen for the r3 put the Peg and the Shifter in a more aggressive riding position.