I can not get my BME-50 clone to run as smooth as I want. It goes out of balance at about 4800 rpm. It is a harmoninc thing that does smooth out a bit at higher RPMs. The crank, hub and prop are all dial indicated within a couple of thousands. I did that on a lathe with the crank/hub assembled. The hub is true to a thousandth, I just made a new hub today, it is straight. The props are Vess and I did balance those down to the gnats's behind. The crank bearings are in good shape. The timing is correct and has no effect on this.

So, I took a Menz prop that was previously drilled for a six hole hub. I added lead to one of the holes, thereby purposly making a heavy side. I ran a marker aginast the hub while running 4800 rpm to find the high side. I installed the prop with the lead opposite the high side of vibration. The vibration got better.

Could the crank have been made put of balance? Would the original chain saw flywheel have been made to dynamicaly balance the whole system? If so should I figure out how much to remove from the hub to pull it into balance using lead weights?

On a happy note, the pitts muffler for the CRRC 40 kit engine fits the BME-50 perfectly.

All singles vibrate, its the nature of the beast. Savvy designers can chose the rpm. Most of the chainsaw engines have a vibration node in the 3-4k range, but are smother at full throttle where they run for hours.
I think that if you look at your engine you will see that you have added weight to the counter weight. In rare cases adding weight opposite does work.
At the dawn of giant scale several people made good $$ "overbalancing" the Q35's

My Alpina A330 has an external adjustable balance weight just behind the flywheel. It is converted from an Italian chainsaw.

Harmonic imbalance is a combination of tortional reaction and engine imbalance but I doubt is is your problem here. You say you are a thou here and a thou there and although it may not seem much, it will have the effect you describe. Tkg was right in his quote about vibration and how it tends to smoooth out at a particular rpm which is why they re-balance stock engines when they are to be used at higher rpm. All engines vibrate at particular rev ranges and oddly enough, odd number cylinder engines are smoother than even numbered cylinder.Normally external balance of a crankshaft is avoided in favour of internal balancing as the former tends to add another dimension of imbalance.
In short, your hubs need to be true turned. I have heard of a Gnats whisker having been used many times before as a measurement , even used it myself to describe a small amount, but so far cannot track down any reference anywhere as to the actual size. Maybe it is rellavent to the job at hand and therefore varies.