Jim,
Have you looked at these encoders yet?
http://www.usdigital.com/products/e6/
For a little more you can get something that can slip over any size of shaft (add the -h for a through hole).
949 used them on 2006, we are going to use them this year, 492 has also used them as well.
The only draw back is that you have to keep the count down to 200 and under (100 for this year). Any thing higher and the Robot Controller is just counting ticks.
If you order from them, you get all the tools you need to mount them to the gear box with the exception of the centering tool, You will need to order a centering tool with the first order, however you will only need one centering tool per shaft size you use.
-Jim