I doubt you really need to send these things off for 3D scanning. If you did, you shouldn't expect the scanning company to send you a G-code file that will work on your machine. They would send you a 3D model; you would use your own CAM software to generate G-code from that and post-process it for your machine. I can't see the texture in that little image, but usually they're rather simple patterns of cuts you can lay out pretty easily as a series of lines in a CAD program.
1/32" isn't too hard a tolerance to hit with even a low-quality CNC machine, if it's set up correctly. You would generally set your blank in some kind of fixture, so you can clamp it down securely outside the cut zone and your results would be repeatable. You zero the tool to the same origin as is set in the CAM program, which usually follows the one set in CAD, and zero the Z axis to the top of the material you're cutting. If you need to flip the stock over to mill the other side, you should set all that up in the CAM program and make your fixture so that it keeps everything in registration.