First of all let me say I like your setup, those components should make for an excellent running engine. They appear to be well matched; I assume you are also using high compression pistons and a good free flowing exhaust. I am most envious.
The type of problem you described can be frustrating to diagnose and resolve. I suggest you reestablish or basically confirm baseline tuning. I would check; valve clearance, initial timing and points gap (not for you). Sounds like the plugs, wires etc are new; so I would not mess with these for now. And last I would confirm the carburetor tuning.
I know it’s a lot of work to do these things, but sometimes to find what is wrong; you have to find out is not wrong.
After doing these things I would connect a vacuum gage to the intake manifold and actually monitor it during driving conditions. There are some excellent web sites describing how to diagnose using a vacuum gage.
As a sidebar I had a problem with a recent rebuild where the engine would randomly misfire from 1500 to 2000RPMs under light load and ran out of power at 5000RPMs. After doing the above I finally turned to the exhaust, a new Monza system; it turned out that it was too restrictive for the longer duration cam causing vacuum fluctuations at low RPMs and excessive backpressure at high RPMs. Replaced the exhaust with no other changes, runs like a bat out of hell to 6,000+RPMs and misfire gone.
I hope this is helpful. Again, I do like your choices!