I went ahead and did a writeup on how to get auto squaring working on the Dremel CNC. Just a note, if your using a clone CNC shield from eBay then you will loose the ability to control the spindle, but with a proper CNC shield, or a ramps board you can have it all.

https://docs.google.com/document/d/1KOMStGTb-w_KqlAyxvKoIVSi_9OebBm97TLjsE9GJBE/edit?usp=sharing

Let me know how this works out for you if you try it.