my two cents - so take it for whats its worth!
Re: question 1 - You betcha! MACH2 will let you configure the motor/driver/ballscrew combination independantly for each axis. Take a moment and download the trial version and I think you'll be impressed! I bought it and am still working out the second question you have re steppermotors. Working through steps per unit (inch), velocity, acceleration, pulse width, etc - trying to make the squares come out square!
So far I'm up and running - cutting blue styro while sorting things out - making noise and chips! Art (the orgin of the MACH2) has been very helpful and considerate in getting it all setup too.
The manual is EXTENSIVE - maybe 200 plus pages so well documented and a good read. A few rough patches - but hey so has MSoft!
Jim
ps - I don't work for the guy - just a satisified customer!
I did the eBay scrounge thing too and settled on using some Acme threadded rod for x and y for now. Tollerance seem pretty good but will know better when all "dialed-in".