[Mr Jody]

In the world of intake manifolds, the Victor Jr. does stand a bit tall. A check of the Edelbrock catalog shows the following carburetor pad heights (at the middle of the pad).

Victor Jr. 5.50”
RPM Air Gap 4.90”
Performer RPM 4.90”
Torker II 4.59”
Performer 3.72”

The RPM Air Gap and Performer RPM, at 0.600" shorter than the Victor Jr. would get you very close to the 5/8" (0.625”) that you say you need. The others would give you that and then some.

Grasping at straws here, but with your 289 being somewhat of a prototype, could it be that the motor mounts might be higher on the frame than on a 427 and later 289 models? But then trying to change that might open up a whole different can of worms.

As somewhat of a last resort, changing the intake manifold would give you the added clearance, or perhaps a smaller distributor to allow the dropped bottom cleaner to be used, but it does seem like doing something with the air cleaner (something shorter than 2”?) would be possible and least expensive approach.