No, you won't have to rejet.......
My bike has been modified and I don't run the prefilter.
In your case where the bike is stock, I think it is best for you to run the prefilter.
Someone with better memory than mine will jump in here however....
DO NOT do any mods to the air box. If ya do, make damn sure ya have a complete one to put on it after she runs crappy on ya. Don't ask how I know that.
If anything, get a spacer and longer bolt to raise the front of the tank.
This is a fellow member from Arizona, he has good stuff. The spacer is the 5th item on the page. You will need a bolt just below the bushing. I have #1.
http://www.bigbf.com/product_sale/