@sdp8483 wrote in the comments to announce that he had created a 3D printed alignment jig in order to assemble his own Habit Tracker. 

The design holds a column worth of switches and it both pushes the metal case down as well as ensure the separation between columns is fixed.

Here is a picture of his finished Habit Tracker. The switches do look indeed aligned.

The jig can be downloaded at Sam Perry's thingiverse page here:

https://www.thingiverse.com/thing:3018815