Hah! I have the same problem. A high rise intake manifold that the dyno test showed worked a lot better with a 3/4" spacer on top. Then the carb. Tried a low profile air cleaner, but that interfered with the choke and the fuel inlet. Solution was yet another 1/2" spacer on top of the carb, and a banjo fitting on the fuel inlet.
Putting the air cleaner on, and a bit of clay on the top, showed it was too tall. I flipped the dished top upside down, now there's 1/4" of clearance. I guess that'll have to do.