Pretty good summary there Neale. Another issue is that with replacing the trapezoidal screws with ball screws - and the associated increase in efficiency, unless you lock each axis (good practise, in any cases on a manual machine) you'll likely find that the axis will move under the cutting force under load.

The cogging effect of a stepper connected shouldn't be underestimated - I finally removed my cross-slide hand wheel on my lathe conversion (to replace with MPGs) as I realised that it did not afford the finesse that you normally associate with a manual control (plus, it was a stomach-ache [glad the stand is as tall as it is] if working close to the machine when it decides to do a rapid movement).

OP: Twin shaft is one way - another is a belt drive onto the screw - offsetting the motor away from the screw and allowing the original hand wheel to be retained.

But... think hard about why you want to CNC... and why you want to retain manual control. I stripped my mill (SX2.7 long-bed) of all manual controls - except the quill feed lever.