Unless you bend the shaft, it's not going to be sufficiently out of balance to worry about, and it would be pretty hard to balance the cones. You're much more likely to have vibration from the sort of imbalance that the static balancer can't balance than from any minute shaft or cone imperfection.
As was already said, just get it right statically and go fly!
However, If you want it closer to being balanced, Balance each cone separately. Put the shaft into the balancer with one cone on it, wait until it stops spinning, make a mark on the top edge of the cone. Spin the shaft and cone a couple more times to verify that it stops in that same spot each time. If it does, then the side opposite the mark is the heavy side. Sand a little off the heavy side checking for balance every few strokes of sand paper until it is balanced. Take that cone off the shaft and repeat with the other cone. After you have done that, you have made it as precise as it's going to get.
But this still fails to address the dynamic imbalance of slightly different blade pitch side-to-side, or front-to-rear weight difference, both of which would very likely cause much more vibration than the milligrams of difference in cone weight. Also, you can get some very precisely made aluminum cones from a DuBro balancer.
I don't think it is possible to completely eliminate viabration in a model aircraft. Even if you could balance the prop perfectly, you would still have a mass produced engine turning that prop.
High performance, and racing engines are usually precision balanced by their builder. Each part is carefully weighed, then a corrosponding weight is attached to the crankshaft, then the crankshaft is spun and checked for balance. If the balance is off (almost always) holes are drilled in the crank balance to reduce weight, or to contain added weight as necessary, until the rotating mass is in balance. ( I should add that the weight used to represent the piston & connecting rod during balancing doesn't actually weigh the same as the parts it represents)
Your engine on the other hand contains a piston, from a bin of pistons, that weigh somewhere between weight X and weight Y. That piston is attached to a connecting rod, from a bin of connecting rods, that weigh between weight V and weight W. They are in turn attached to a crankshaft that is balanced with an approximate weight, somewhere in the middle of a range represented by the weight of the lightest possible piston and connecting rod, and the heaviest possible piston and connection rod. This produces an engine that is reasonable balanced for most users.
Precision balancing a engine is time consuming. and relatively expensive. The old saying goes " Speed costs money. How fast do you want to go?"
My advise is to balance the prop as well as you can. Bolt it to the engine an run it. If you think there is to much vibration, loosen the prop and rotate it to a different location in relation to the connecting rod, and run it again, maybe you will find a location where the combination vibrates less. If you still aren,t happy with the amount of vibration you are getting, use some kind of isolation mount to keep the vibration from the airframe.
For a better explanation of what is involved in balancing look at...
The article does a good job of explaining the principles of balancing.
Assuming you have made sure there are no structural problems (loose motor mount, firewall, etc) and you have balanced the prop as best you can, then try moving the prop around the crankshaft in about 30 degree increments. You might find a sweet spot where the inherent vibration is minimal.