I agree. Ive always noticed that on my sp1. The right side fits a bit closer. However, it doesnt come close to any clearence issues with swingarm.
Can you post a picture of the hole your talking about? How much clearance do you have? Considering the motion of the swingarm, i would guestimate you need about an inch. I just looked at mine.
If its real close, i would take of both side fairings, and check all the header connections. There's 5 or 6 in all, depending on sp1 or sp2. Use a little penetrating oil where you can, cause the bolts can be very stubborn and you dont wanna twist em off. Once the connections are a little loose, you can see if the system wiggles back into proper place, or close to it. Should probably look up the torque settings when tightening up, cause i remember them being lighter than i expected.
While you got fairings off, look Real close for other damage, especially around the rad area you mentioned. Any leaks?
Good luck, try to get a pic up.