Here is a post that identifies an area that is of concern to me since I have had similar issues with a lot of different bikes over the years.
http://www.advrider.com/forums/showthread.php?t=329337&page=1149
Take a look at the third picture down in the link above--nothing good comes of the shifter entering the side case
So being proactive I have attempted the following mod:
Cut a pattern
Transfer
Cut
Check
Finish
Check fit
Silicone
Only concern
I will give it an ops check this weekend and see how it works out--if nothing else I will remove it and carry it in my tail pack with some liquid steel and use it as a patch if I puncture the side case at some point. My hope is that it will just ride along where it is and take the hit if I dump the bike wrong.