Maybe check to see if the flywheel is seated properly on the crank? If the key gets caught in there, sometimes it can keep the flywheel from going down all the way. But then, you would have an alignment problem with the starter gear.
It is getting late in the season for this, but you could send the crank/rod/piston and counterweights to Doc and have him balance it.
I don't have any experience with one that does not have our brass balance weights, so I wouldn't know if what you are feeling is normal or not, but the word I hear is that the engine should have better balance with the brass weights than without.
You do have them pinned to the crank counterweights, right?