With only 3 cylinders, you'll have an easier time locating the problem than a 4 or 6 cylinder engine ! Starting with the spark plugs and plug wires was a good idea. If you have ignition points and a condenser, try replacing them next. Make sure there's no dirt on top of the coil or distributor cap.
Clean the distributor cap inside and out, and look for cracks. You might try removing ( and grounding) one plug wire at a time to see which cylinder is weak. Any problem in the fuel and air intake system can cause rough running , including water getting into the air or fuel. As mentioned above, a sticking valve can cause rough running, so you might want to check the valve lash . An ample amount of a top cylinder oil added to the fuel ( I use Marvel Mystery Oil) , and an intake system fuel cleaner ( I use Chevron Techron) may solve the problem after a few hours of running. My Ferguson TO-35 has lots of hours on it, and very worn cylinder liners and piston rings, but still runs smoothly . It does burn some oil, and leaks some too, but that's ok for a tractor that gets only occasional and medium duty use.
