I'm starting to plan the focus mechanism first, since I just received the focus steppers this week. Since the stepper motors are geared and don't allow free motion unpowered like most steppers, I need to use either a friction drive of some sort or be able to engage/disengage the motor if I want to use the microscope manually. My initial plan is to use a simple wheel friction drive against the fine tune focus knob. Hopefully the friction of this drive mechanism would be just enough to engage the focus knob but allow free motion when it is not in use.

Here is the exact Lego wheel I purchased:

http://www.bricklink.com/v2/catalog/catalogitem.page?P=4185#T=S&O={}

http://www.bricklink.com/v2/catalog/catalogitem.page?P=70162#T=S&O={}

I will 3D print an adapter to go from the stepper motor to the Lego wheel.