You can draw your parts in Autocad.
Then you need a CAM program to translate the drawing into G code. Search this site for recommendations. Vetric makes some lower cost software.
Mach 3 will run the G code file and send commands out to your motors to move your machine. Typically you use the parallel port to do this along with a motor controller like the Geckodrive G540 (if it is appropriate for your motors - it might be overkill if they're small). However if you are dying for USB, you could use a smooth stepper for additional expense. Then you would go from that to the G540.
CNC mill build thread: http://www.cnczone.com/forums/vertical_mill_lathe_project_log/110305-gantry_mill.html