Air Cleaner issues

I have a 340 with an Eddy Airgap, 1" spacer and Holley 650 so basically the same setup as you. My 14" drop base is about 1 1/2" drop. My hood closes fine. ('69 Dart). It is very close. I run a torque strap so the engine torqueing doesn't dimple the hood.
Remove the 1" spacer to see if that helps. Then you will know you are within an inch and can get a different drop base or some other mod. Or leave the spacer out.