I'm having a difficult time understanding your hood to air cleaner clearance issue. My 65 with a 351W in it, and a K&N 3" X 14" dropped base air cleaner, and a 3/8" Edelbrock heat insulator, on top of a Performer RPM manifold, still has 1 1/2" hood clearance (measured, using clay). Have you actually measured your clearance? BTW; I was having the same fuel percolation problem and installing the Edelbrock 9266 heat insulator was the cure. You may not need a 1" spacer.
65 GT coupe. 351W. Edelbrock Performer RPM heads, manifold, cam. Toploader. 9" with 3.70 trac-loc. 4 wheel discs. Leather seats. The actual car I learned to drive in over 45 years ago (except for the mods!).