If the engine smoothes out, then a vacuum leak or lean mixture condition is indicated. The manifold gasket may need replacing. I think the overall fuel mixture is fine because the engine only misses at times, so that leads us back to spark. Most ignition parts have been replaced, so I would check for low voltages to the ignition system. The power wire to the distributor should have close to the same voltage as the charging system puts out when the engine is running.
Low voltage can cause misfires.
Look for bad connections or a bad ignition switch. The distributor mounting pad must be clean of paint and corrosion. Contact between the distributor and the engine block is crucial for current flow through the ignition system. Bad contact can cause misfires. Finally, check the distributor advance weights beneath the rotor for free movement.