I think you need to use dwell. Dwell is an electrical measurement of the time the points are actually closed. Since the coil is charging when the points are closed, correct dwell is important.
In my experience, point setting and actual dwell can vary by a significant amount. If the dist. bushings and point cam are in good condition, then point gap and dwell should match. When dist bushings wear, the slop can allow the cam to move away from the points,changing the actual gap under running conditions. Sounds like what you are describing.
The worst case I ever saw was a 58**** with a 292.
When the points were gapped to .016 the engine wouldnt start. If the points were set to around .005, the engine would run. The dwell at .016 was nonexistent (meter didn't read) but at .005 it was around 22 or so. New (rebuilt) dist. cured the problem.
My 5 cents
Curly
