You can leave the AIS system in place. What I did was to put an extra clamp on the tube that connects to the bottom of the airbox. Then, I pushed into the tube an electrical wire nut a couple inches. I tightened the clamp below the nut so it couldn't slip by. Then, I topped off the tube with silicone, put it back on the airbox and clamped it in place.
To do this, you have to lift the tank, remove the airbox cover, remove the stacks which releases the bottom of the airbox and allows access to the tube which is attached to the underside of the airbox on the left/clutch side. Expect about an hour but do it after your riding day is over. You'll want the silicone to cure over night.
Essentially, what ever you can snugly fit into the hose and clamp in place. I don't think I needed the silicone but I wanted to be sure it was sealed.
To remove the whole thing, you need to replace the plates on the valve cover with either Ivan's, Copperdog's or block the holes where the tubes would normally connect. Some have even used JB Weld and welded a penny under the plate to cover the hole.