Mounting Encoders AR3?

Hi Chris, I've purchased all the parts to upgrade my AR2 to AR3 but have run into a issue right at the start. Your AR3 Robot Manuel shows additional mounting holes for the encoders on the back of the steppers. My steppers do not have additional mounting holes in the back. I'm assuming that I need to drill/tap these myself? I don't see anywhere in the instructions where it directs me to do this... I'm also confused on the length of the shaft out the back... mine all seem short. The instructions included with the encoder are pretty basic and do not really help to solve this issue.

Thanks!