So I ordered my PCBs and components, and when they arrived I realized I named some of the nets incorrectly and never connected the traces. I also used the wrong digital pins for interrupts on the encoder, and the wrong PWM pin for the MOSFET. It turns out that the Atmega328p has a 16 bit PWM capability on pins 9 and 10. So I completely reworked the circuit again, and added a quadrature to step-dir converter as well as a few other changes. Below is a picture of the schematic, and the new files are on my Github Repository.