This is just an update to my question about a Pertronix distributor being to high and interfering with the 2 x 4 air cleaner. I hope it might help someone in the future.
The application is a 63 Galaxie with a factory 2 X 4 Intake (March 63 casting), Quick Fuel carbs, Blue Thunder 2 x 4 Air Cleaner assembly and a Pertronix III Billet Distributor. I mention the QF Carbs and BT Air Cleaner just because I'm not sure if Holley's and the Ford air cleaner would make any difference.
The distributor is definitely higher and will hold the air cleaner base up in the front. Trans-Dapt makes a 2" Phenolic plastic spacer, part # 2532, that was machined down to 1.288"which brought the air cleaner base to almost touching the plug wires on the distributor cap. Phenolic plastic is not fun to machine, it makes a rather evil dusty mess, it helps to have someone sucking the material up with a shop vacuum while machining. Wilson makes some really nice aluminum spacers you can get in 1/8" increments which may have worked out but they cost $100+ a piece compared to $40 for the Trans-Dapt spacers and I still would have needed to do some machining. I also had to go from the 2.25" to the 1.75" Blue Thunder air filter element. At that point the air cleaner fastened down properly and their was minimal clearance between the ends (oval part) of the air cleaner and the underside reinforcement structure of the hood. I thought I was done but after a couple hundred miles the very front edge of the oval part of the air cleaner top showed some polishing effects from contacting the underside reinforcement structure. It had clearance when checked but apparently the engine moves just to enough to make some contact. I resolved this by slightly reworking the structure with a couple of ball peen hammers. I put some tape on the structure and after a few hundred more miles the tape is untouched so it appears to be resolved.
There is absolutely minimal clearance between the Pertronix III billet distributor cap to air cleaner base and the air cleaner top and hood but it does just make it.