Save yourself some pain and leave the undriven end of each ballscrew unsupported.
On a small machine you won't see any rod whip and it makes it HEAPS easier to line everything up.
The screw manufacturer will have a table for the maximum unsupported length of screw for a given RPM... Look it up if you are unsure..
I disagree with you on that one. I tried that and ended up with Screw related Harmonics which marred the finish of the item I was machining.
My method for lining every thing up;
Make sure the BallNut is secured in the intended centre of the BallScrew Axis.
When fabricating the End Plates which hold the Bearing, make the Mounting Holes a mm oversized. (eg 6mm Bolts, use 7mm Holes).
Bolt everything together so that the End Plates can move laterally.
Drive the Axis to the Motor end of it's travel and nip up the Mounting Bolts at that end.
Drive the Axis to the other end of it's travel and nip up the Mounting Bolts at that end as well.
Drive the Axis back and forth between limits and check that there is no binding anywhere.
If all is well, tighten the Bolts fully, and repeat for the other Axes.
I've converted two Mills and built a CNC Router from scratch, and have used this method with success on all three.