Alright, second round with the controller. I think I have everything where it should go, if a couple of folks want to go over it with a critical eye to make sure I didn't swap a resistor here or there it would be appreciated. This was also a quick render, once everything is done I can run one out with better quality.
Don I did manage to move the diode designators that you commented on, I also tried to figure out something for the ceramic capacitors C49-54 that sit between RN41 and the discovery board riser but there just doesn't seem a good way to do it unless I add then as a text layer in the finished image, possibly overlaid on the riser. If anyone has ideas I'm more than willing to try things.