Yes, I used your .dxf files. I changed the outlines to polylines and then offset them the radius of the end mill used, usually 1/8" dia.
The CNC software I use is Mach3. It is great stuff and works equally as well on wood routers. You can see it at: http://www.machsupport.com/artsoft/index/index.htm
The center holes are probably off due to the inaccuracy or backlash of the mill table locating screws. I'm not a purist so I put up with it. My next clock, I will cut the gears teeth first then (by using an edge finder on the gear tips), relocate the center then drill the hole.
As far as problem solving, I have been a design engineer much of my professional lilfe, now retired. I worked for many airplane companies and was directly involved the early space program. Remember Mercury, Gemini and Appolo? Coincedently enough, my first assignment out of college was the design of "A satalight clock." However it was NOT made out of wood!!! The modification for the timing is simple. See attached. It is a threaded rod with two nuts that are tightened slighlty. They close the fork pallets. Apparantly just enough to slow the clock. The fork is made out of Delrrin. One of my inabilities is photography. But I will take a few more better pictures after the holidays.
Thanks for your interest.from South Florida. --