Here is a part that mostly works (with the warning that I don't know why it works 
). All I did was group the components in breadboard because with only the connector present it worked, indicating something in the non connector part of breadboard was causing the problem. I was intending on removing the components one at a time til it worked to identify which one it is, but to my suprise when I tried it it seemed to work. I think the bus stuff may have problems, but I'll look at the tomorrow. Also the connector holes are .040 when they should really be .038 but thats minor. It exports on .1 centers correctly in the gerber which is the important part.
Raspberry Pi Zero_fixed.fzpz (46.3 KB)
Peter