Hi All,
A simple method for compensating for slight misalignments is use a
length of vinyl tubing which is a snug fit on the ballscrew. You will
likely have to machine a bushing to fit on the stepper motor shaft.
Since you can do this with one setup on the lathe the holes will be
concentric and the only "gotcha" is the fit of the bushing on the
stepper motor shaft. Try for a slight interference fit and use
Loctite grade B bearing mount on final assembly.
Some further thoughts on PCB drills.
If you cast your machine base out of 95% ( by weight ) mason's sand
and 5% Clark's liquid epoxy (
http://www.clarkcraft.com/ ) you'll a
very strong base that can topped with a final thin liquid epoxy coat
to level everything out at a cost well under $100.
If you make a vacuum tight box under a work surface of MDF a shop vac
will hold the PCB tightly in place. Since you will need some sort of
dust pickup for the drill it makes sense to let the shop vac be your
clamp.