I had the same clearance problem with the new mounts, the long Cobra oval cleaner and a Performer RPM manifold. My clearance problem was at the front of the air cleaner since it protruded farther than the hood scoop towards the front of the car....I had plenty of room towards the firewall. I took the base of the air cleaner which has a one inch or larger ring that raises it up off the carb and shaved the front edge tapering the cut at an angle towards the rear of the cleaner. This tipped the front of the cleaner down over an inch in the front giving me the clearance that I needed and yet still left plenty of clearance in the rear. The same thing worked on Weiand Stealth manifold...( almost the same as the performer RPM).
Worked great for me....Hope it helps for you.
Bill
I'll see if I can get a decent photo and attach....