fix height of upright z spacer and tidy code

This MR fixes the bug in the upright z-spacer that is identified in #355 (closed).
Also some code tidying.

• Correct parameterisation of the spacer height and place the bottom on the z=0 plane.
• Parameterise the code more clearly
• Delete repeated hole cuts
• Other code tidying

Added (64d58a67 and 5cfa159f):

• Build the part in place (at the height of the illumination dovetail mount). This simplifies the translations, will simplify rendering.

closes #355 (closed)