On paper, it's pretty simple. Get a dial indicator, a way to mount it, position it against the shaft and rotate.
In practice, as shown in Drago's picture you have to make sure the indicator is in the right position and doesn't move. You can spend some $$ on a precision tool you'll only use once unless you can borrow one.
It was at this stage in my gear drive conversion that I started thinking it would be a lot easier--and safer--to turn the project over to somebody who has better tools than me. It turned out my runout was fine.
Last edited by SickRick; 11-15-2012 at 08:13 AM.