The problem turned out to be the bearing in the bottom end of the rod is migrating to the back of the engine.
I was able to push it back into place with a piece of brass tubing and a smack with the hammer. I don't guess it will stay where it is supposed to be. Its probably pressed in but in my case it is not a tight enough fit to keep it in place. The only real cure will be a new rod that has the correct fit. I don't suppose lock tite would stand up to the temperature in there.
Does anyone know if there is anything I could put on there to keep it in place?