Bruce is likely right about the timing chain, with the plastic teeth being on the edge.
Maybe you should take a look at the rocker arms. Even though you did a top overhaul a short time ago, the stock rockers are a weak point in these engines.
I had one that the bolt that holds a pair of those came loose. Shouldn't be too difficult to take a look. We are still trying to get some ideas here
Did you replace the coil? Heat related problems could affect the coil on some ignitions with points. The old style coils were oil filled, and prone to heat problems as I remember. The spark is strongest at idle, because of longer coil saturation, and any carbon tracks on the coil tower or anywhere in the cap will affect the way it runs.
You could also start it up after dark, and see if any stray arcing is evident in the ignition system.
If you suspect an intake manifold leak anywhere, like at the cylinders that are affected, dribbling a few drops of gasoline along the manifold gasket edge will bring RPM up if there is a vacuum leak.