[Alan Roehrich]

Ben, can the miss be isolated to one or two cylinders, or is it just a miss that moves from cylinder to cylinder?

With a completely different ignition system and carburetor having been tried, if I read correctly, you're starting to move toward a mechanical problem, as much as that is something you do not want to hear. I'd do a compression test, check the lash, check the lobe lift, hook an undampened vacuum gauge to a manifold vacuum source, and check the valve springs.

You might try a fresh set of slightly (1-2 steps) hotter plugs, with a gap in the 0.026" range.

Have you hooked a volt meter to the various 12 volt positive inputs to the ignition system? You might look for a voltage drop when the miss is happening.