Part seems to have "internal connections"

parts help
2

You look to have not changed the bus definitions from the atmega32u4-qfn2 part you cloned from (the dip 40x2 part would probably be a better starting point though.) In the fzp file this section is not correct:

  <buses>
    <bus id="AVCC">
      <nodeMember connectorId="connector43"/>
      <nodeMember connectorId="connector23"/>
    </bus>
    <bus id="VCC">
      <nodeMember connectorId="connector33"/>
      <nodeMember connectorId="connector13"/>
    </bus>
    <bus id="GND">
      <nodeMember connectorId="connector42"/>
      <nodeMember connectorId="connector34"/>
      <nodeMember connectorId="connector22"/>
      <nodeMember connectorId="connector14"/>
    </bus>
  </buses>

presumably it is correct for the atmega32u4. I would start from the 40x2 dip part and replace the pcb svg with the one you used in this part (checking the pin numbers when you are done.) The following tutorials on parts making may help as well.

Peter