@SkyeFire There are no stupid questions. The registration holes are drilled first using a corner of the stock as zero. Model your stock, use its center as reference and make the holes. Once they are done, these become your new reference for zero. I use the quick position center as my new x, y zero. The holes are equidistant from the center of the stock.
I learned a lot with this project. Being able to simulate jobs has allowed me to study different strategies and see their impact on time and quality. I highly recommend learning Fusion 360. It’s free and very powerful.