Solved: MySQL Server is Running on the Wrong Port on Mac OS X 10.10 (Yosemite), And It's Not The Configuration File!

I recently had trouble with a fresh installation of MySQL on Mac OS X 10.10 (Yosemite), and it wasn’t an issue with my configuration file. This is my story of discovering why I couldn’t connect to my local database server, and what I did to get things working again.