A gearbox is about the hardest common place mechanical item to design/make. It takes expert skill to make one and designing one as your first venture into drawing blueprints is similar to starting out by designing an FPGA board and programming it as your first project. I can guarantee you that your design will fail when you get it back (similar to PCBs!)...and it will cost a lot more than PCBs.
There is no set way in how they charge you. It depends on the material, how easy it is to machine, and what exactly you want done to it, and how much machining you want done to it, and how much material needs to be machined. It's all over the place.
CAD programs are also not free (ones that can design things like gearboxes anyways). Downright through-the-roof expensive I would say. Just like OrCAD or Altium eMachineshop is the only one I know of with free CAD that is permanently linked to their service and no other (like PCBExpress...or was it EXpressPCB?), but I'm not sure you can design something like a gearbox with it.
If you really want a custom one, either learn the trade (obvious time disadvantage there, not to mention lots of little projects to build yourself up to a gearbox) or hire someone to do it for you (expensive, but it would easily cost you the same in mistakes, and far more time on your part).
What do you need? Can you not find anything like it from battlebots gearboxes (like
http://www.robotcombat.com)? Those things already cost like $500 a piece and though they aren't mass produced, they aren't singleshot (and thus cheaper) like yours will be either.
Guys like
http://www.rc4wd.com might also design and build it for you...at a price.
What's your budget? FOr something like a gearbox the size of your first, it could easily be $600 in machining costs and maybe 3x that for design labour (wild guess). I got a quote for a pair of solid RC axles from them (no custom gears involved like your gearbox will likely be) as $600~1500 (something like that), and they were not charging me for all the design labour involved.