Is your lower pan an original factory piece or a repo? If it is a repo, I would cut and modify it to keep it at stock height. ALOT less headaches, trust me!! I put a performer RPM manifold on 69 Goat, it is about 3/4" taller than stock. I used the lower Ram Air pan with the foam at the stock height, it looked like crap when the hood was open, and I had to really push down to get the hood to close. It also pushed up on the rear of the hood, if your hood hinges have any slop at all, this will show you and everyone else!! I ended up cutting the foam down by 3/4" and the glued the cut side to the pan, so the nice machine cut side is up. For the air cleaner/filter, 2" is too tall and WILL hit the upper pan, anything smaller will be too short and will choke the carb. I am not going to tell how I fixed that issue unless you ask, MANY purists will cringe when they hear what I did!!
I did run one of the K&N filter tops. I don't care how well the Ram Air setup is built and installed, They are NOT watertight, even with the flappers closed tight. So all of the water that gets past the scoops when it rains or when you wash the car goes right through the filter top and into your engine!! Trust me, I know, don't use one with RA!