Just a guess.
But, if you are still running points, you could check that the area behind the points cover is dry and teh gasket seal is still doing its job. If there is water/condensation inside there, it turns to vapor as the bike warms up, then it can deposit on parts that are still cool inside, like the points. Intermitantly shorts them out and causes misfires.
Or, maybe you have some water/ condensation in the gas. It will collect in the low points of the tank/carbs and choose it own time as to when it finds the jets; like after it sloshes a bit in the tank. Or, if it wanders over from the side of the float bowl. Drain a bit (or all) from the bottom of carb float bowls into a clean shallow pan. If you find something other than gas then you're on track for a cause.
Check to see if your gas tank vent is clear. If not, as fuel is used, a partial vacuum can build up and stop flow to the carbs.
Well, there's some ideas...
Cheers,