Try checking the fire on the cylinder that is missing with a inductive timing light. If you have intermittent fire, I would replace the coil for that cylinder as it may have developed a heat problem. You could also swap the coil to see if the miss moves. One of the coil could be failing because of heat. I had this same thing happen on a 22 HP Command engine. I thought the engine was tried as it was on a zero turn mower the local school used that had POOR air filter maintenance. I install a new engine. Later after seeing the inside a a single cylinder command engine that had eaten WAY more dirt that the v-twin had I took the V-twin apart. I could find NOTHING wrong with it. Later because of some operator errors, this engine was put back on the mower it came from. It seems to be running well. I do not know WHAT made it run poorly in it's earlier life.