I just tested my new focus stacking system and it was fairly successful. In the end I mounted the subject on the scanner and just triggered the camera manually using the shutter release button. The scanner ticks loudly every time the arm moves so it wasn't too hard to know when to release the shutter.
I used this python script to drive the scanner. The camera setup was a Canon 5d MkII with a Canon MP-E 5x macro lens. The camera was just resting on a box and working in auto mode. The battery was stuck to the arm of the scanner with a bit of blue tack to stop it wobbling.
Here are a few sample images:
This is the focus stacked image, compiled by Helicon Focus:
There's some strange fuzzy stuff going on at the top, but otherwise that seems to have been fairly successful.
This post follows on from Focus Stacking - Connecting the wires.
The next page in the series is Focus Stacking Coins of the Realm.