I don't think the scoops have to come loose, whatsoever, in order to get the Gen II air box open ONCE the top Faux cover is off. (both our Gen II's have the big air kits and no longer have the airbox inside)
You will have to remove a single screw on the SS top cover around the Faux cover instrumentation. That will expose four(4) more screws inside that must be removed. These four are fairly close together. Two hold the instrumentation up flush with the Faux cover, and the other two hold the faux cover downward. Then there are the two forward screws at the very front of the Faux cover, one on either side of the steering neck. You will have to rotate the steering from side to side to get each of those out. You already said you have the lower, rear two bolts out of the cover.
Now as you are liftling from the back of the cover, you will want to press down on the rubber inserts around two of the inner, previously hidden bolts near the instrumentation. This will keep those grommets in their proper place on the bike as the cover comes off.
GET THEE to a service manual asap. It comes in very handy.