Do yourself a favor. Fender removal kit and air box removal would make things a lot cleaner. You'll be surprised how much more room you have without that semi truck air box. This isn't the best pic but it gives you an idea.

Even a short fender like the one I am using (Moto Twin-dear departed Moto-Twin) Should give you the clearance you need. I'm not sure about stock.
I love the Ikon adjustable shocks but if you are looking to lower the bike with the shocks, check with Bella Corse or newbonneville and see what they recommend. They both have good experience with our bikes and will back up what they sell.