I also have 4" extensions. When I put them on I had a SS Custom Cycle K&N which is very narrow, so I didn't even notice it. Recently I went back to the stock filter housing (didn't like the exposed filter in the rain) and I did notice my leg hitting the filter housing. I've been riding it for a while and have just gotton used to it. Not sure if you would want to move floorboard out more for 2 reasons.
1) You will have less lean angle before your floorboards hit pavement.
2) When you added the extensions, you already have misalignment from the brake pedal to the brake cylinder by the thickness of your extensions (~5/16"). There is some flexability to the brake rod, but I wouldn't add 1/2" spacer to the floorboard unless you make the brake rod offset.
If you like the looks of the aftermarket exposed filters like I had, most of them are much narrower than the stock air box, but your going to pay $250-300 for a new one.