I think I found all the parts and layed out everything again. I learned that I had the wrong model for the Ethernet connectors when I went and read the manual for the ones I'm looking at.
I talked to my boss for the summer who does electronics, and he suggested the diode to keep the CPU running across quick spikes.
Hopefully the BOM that I made is useful. I can update it if needed to a different format.
Thanks for all the help so far!