Three things could possibly be causing your overheating problem. More than likely a lean running condition on that cylinder, but could possibly be cooling fins covered in dirt, internal timi problems or even a plugged muffler. If it came into the shop this is what I would be doing, in this order.
1. Pull the spark plug on the hot cylinder and check the color. If it is a bright white it would indicate a lean running condition. This may sound stupid, but I’ve put an old car boned plug into the cylinder and run the unit. If the carbon burns off we know we have a hot running cylinder.
2. Remove the shroud and make sure the cooling fins around that cylinder are clean.
3. With the shroud off I would start the engine and take a can of carb cleaner and spray every gasket between the carb and block, looking for an engine speed change. If it does change, you are sucking air creating a lean running condition. Also spray the entire intake manifold as it may have a hole or crack in it.
4. Nothing found yet I would recheck my valve clearances. Also, you should have some oil in the valve cover when you remove it. Oil is also a cooling agent and no oil means we need to check why.
5. Finally I would pull the muffler looking to see if it has any obstructions, not allowing exhaust gases to escape properly. Compressed air is your friend here, don’t rely on your eyes, mud dubbers have been found to have plugged them up.
From your description I don’t think you have an ignition problem, but I’ve been wrong in the passed. If all these steps fail I’d being looking at internal problems, starting with the head.
This is just how I would tackle this problem, but there are others who say I’m just an old fart and there are better ways to troubleshoot this problem, so don’t rely 100% n this post.