I had a similar thing happen to me. If your plugs are good AND the right ones (mine weren't) and your points look good (properly gaped and not pitted), then pull the plug caps off the wires and look for corrosion in there. If you see green, clean the spike in the cap and trim back the wire a little at a time until u strike good copper.
Loosing the two cylinders fed from the same coil tho sure smacks of a bad coil, shorted or broken lead wire to the points, or inoperable points.