40-50 holes?! I thought I needed one when I had to drill three boards for each kit I was selling, with a total of about 3000 0.032-inch holes. But I usually only put together 10 kits at a time, and only sold a few hundred of them, total. So I couldn't justify buying one. It only took a little over an hour to drill a set of boards by hand. I used a cheap dr9ill press with a Dremel hose-clamped to it. It wobbled pretty much, so I wrapped a long spring around the tool and connected it to the drill press's post. Perfect!
Eleven years ago, I did investigate designing and building one from scratch. I actually built one but got busy and never mounted the Dremel flexible shaft drive head on it, or hooked it to a computer, although I ran the axes with a pulse generator a few times. I bought a few big old heavy dot-matrix and daisy wheel printers, and a smaller one, for $5 each, and made this: http://fullnet.com/~tomg/gooteecn.htm
. I think maybe I decided the resolution was going to be a little too low. It was something on the order of a tenth of a hole diameter.
So I would probably do it differently, if I tried it again. There are lots of plans and deisgns and ideas for them, available on the web. I also bought a small x-y milling table, back then, from Harbor Freight, that would probably have worked for positioning the board, and would have had better accuracy. I never got around to mounting stepper motors on it, though. For something as light as PCBs, it wouldn't be too hard to build one from scratch. Even plain threaded rod from a hardware store, and some coupling nuts, would work, and could have good-enough accuracy, theoretically, with 200 step per revolution motors and 24 or 32 threads per inch rods. Think about using the concave rollers that are sold as replacements for sliding patio doors, for your x and y platforms to roll on (on smooth rods). Or maybe use drawer slides. There are lots of ways to do it. The basic idea is to attach one or more coupling nuts (long nuts, as in an inch or more of threads) to the platform. Then, when the threaded rod is turned, the platform moves. There is also Acme Rod, and Ballscrew Rod. They are more accurate, and have less backlash, and won't wear out nearly as fast. But the coupling nuts remove almost all of the backlash (and the rest can be removed in software). And they are so cheap that you can simply replace them more often and still come out WAY ahead.
I also bought some old pen-plotters, back then, to see if they could be used, somehow. I believe that some of them would work, to position the board, too (but some are a little flimsy-looking) I even have some old ANALOG plotters, made my HP. Wow those things have scary-fast slew rates. They have manual modes, too, like a giant electric Etch-A-Sketch. Really fun to play with. They would work great, too, and have MUCH stronger motors than the more-modern (but still basically antique) digitally-controlled pen-plotters, like one by Roland that I still have, but would need D-to-A converters and interfacing for computer control.
Thinking about it just now, I would probably try to go with a tabletop-size milling machine, since it could also do so much more. But you have to find out how to tweak the el-cheapo ones, to get rid of run-out, and other sources of inaccuracy. That's all on line, too. Check yahoogroups.com . Everything you need, for ALL of these kinds of projects, in already on there.