Mike,
Nice job so far. I would suggest keeping the mass and inertia down with smaller steppers, especially for your application (EPP).
#1... A CO2 medical laser does not use fiber optics for the delivery system, it will have mirrors inside the arm (at each section joint). It most likely has a very small depth of field (working distance) so you will need to replace the lens. Depending on your gas cost, it may work out cheaper to get a Chinese sealed gas tube and PSU, but the 'free' laser would be a good start.
This particular laser is for busting up stones and uses a cath. to get the laser inside the patient.
#2... There are plenty of options for the driver if you are going the step/direction route. I am guessing you intend to use Mach3 for the software, in which case you could use a DigiSpeed or equivalent to drive the laser power (0-5v signal). There are other options too, but watch out as most of the PWM boards are for spindle controllers and not fast enough for a laser PSU input. An alternative is a custom driver designed for a laser, check out Full Spectrum Eng. or head over to
http://www.buildlog.net/forum/index.php and see the other options.
Thanks for the link. I do plan on running Mach3 initially. I have a back ground with g-code so I think I will be ok. I would like to find a board that can control the steppers and the laser.
#3... The wand would be ok once you replace the final lens, or you could salvage the mirrors from the arm and use them in a more traditional arrangement.
#4... Just the honeycomb will be fine, there shouldn't be any need to paint it.
I will still need the aluminum sheet on top of the MDF right?
Have you laser cut the EPP before? I am surprised you find it better than hot wire, except the obvious internal cuts. In my experience you'll need a long FL lens to get an acceptable straight cut, the standard 50-75mm produce too much beam convergence/divergence )(.
My sheets are .375" x 36" x 48". I do not have a good way to hot wire them. I do have some internal cuts. Right now I am farming out some of my kits to have them water jet cut.
Zax.