Sounds to me like electrical problem. This was a puzzler on car talk once upon a time. Guy drives out with his girlfriend to "make out rock" or something of the sort, they go off into the woods for an hour and to his horror when he returns to the car he discovers his headlights were on the entire time (and are quite dim now). He knew the battery was weak, and her father would be at the door with the shotgun if he didn't get her home on time. The puzzler went on to list some items in the trunk (one of which a pair of pliers) and says he went under the hood, did something, and managed to start the car and get the girlfriend home in time for curfew. The answer to the puzzler was he removed a couple of spark plugs and the engine was able to start with a weak battery
Knowing this story, I would say you've got a weak spark condition. My gut says ignition coil, but if you want to be methodical about this then test all components of the system. Start by inspecting and gapping your plugs, testing resistance across your spark plugs wires, testing the resistance on the primary and secondary circuits on the ignition coil.. the fact that it runs on either cylinder makes me think upstream of that the ignition circuit is ok
