If you use a shaft the same diameter of the prop hub you will get more drag and less accuracy, if you use a smaller shaft you will need a way of centering the prop, something like these:
http://www2.towerhobbies.com/cgi-bin...?&I=LXHY63&P=7
On the other hand there are hand held balancers that are pretty inexpensive like this:
http://www2.towerhobbies.com/cgi-bin...?&I=LXDS10&P=7
You can alway get something like the handheld one and build a frame to hold it.
My balancer uses 2 magnets to suspent the shaft between them.