Here's some more ideas:
I've heard that 289 motor mounts lower a motor about an inch, no verification, though.
I've heard that motor mounts for a Mustang 5.0 convertible lower the motor about 3/4 inch....verified by members of the Mustang forum. You'd have to lower the transmission a like amount to not end up with mismatched pinion angles, but perhaps a convertible transmission mount might lower that item a like amount.
Motor mount bolt holes can be slotted to provide a bit more "lowering"--I did this once when shoehorning a 351C into a Ford Maverick.
The only problem I foresee regarding lowering the engine is that it may cause the sidepipes to ride a bit low. If yours are slip-fit style, then lopping a bit off at the union might just cure that.
The carb mounting pad on the intake manifold can be milled to give even more space for an acceptable air cleaner.....probably a good option on a high rise single plane manifold or an Air-Gap manifold.
I can see lowering the engine might not be a popular option on an already nicely completed ERA.......but, it might work if it is the only option.
Cheers from Dugly