Bryan,
1. Minimum computer? It depends on the performance you need. I would not use anything under 1.2 Mhz. For high speed (45khz) and enhanced pulsing, use a high end computer.
2. Mach version? Use Mach3, it is mature, safe, stable, tested, robust, supported, full of features, etc…
3. Pinouts: You can assign them freely. On port one, output pins 1,2,3,4,5,6,7,8,9,14,16,17 and input pins 10,11,12,13,15. On port two output pins are 1,2,3,4,5,6,7,8,9,14,16,17 Or, 1,14,16,1. Input pins 10,11,12,13,15. Or 2,3,4,5,6,7,8,9,10,11,12,13,1. On the second port you may choose to use pins 2-9 for input, that way you can use lots of inputs. Check out my site, I think there is info that you will find useful for your setup.
http://cnc4pc.comArturo Duncan