I think you might have to go to a custom drop base air cleaner. I don't think one would be hard to make for a Holley, given the circular shape of the top of the carby. I would go and buy a standard 14" air cleaner housing and start from there(assuming that this cleaner will clear other engine bay stuff like brake master cylinder/booster etc). Take some measurements and keep as much height above the carby as possible, after spending so much on the motor, you don't want to choke its performance with the air cleaner.
I ran into similar problems putting an air filter onto one of my earlier setups with a Weber 34ADM on an adapter back when I was running petrol. I tried a Lynx/Ramflo filter but even that would not clear the hood. In the end, I did a cut, shut and fibreglass job to make a custom cold air intake for it. While the shape of the intake was really good, I only had an inch or so above the top of the carby, which we found out on the dyno was restricting the airflow and causing the mixture to go rich. I picked up 3-4kw at the wheels by removing the air filter.
As far as I know, there are no off the shelf parts for it, so I would look at designing the best custom setup possible. Good luck with the motor, I hope to hear it running soon.
Brett.