@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: