So after some monkeying around this is what worked. This is a combination of these threads:
The serial port is /dev/ttyAMA0 and does not appear in the Arduino IDE. You can use : ‘ln -sf /dev/ttyAMA0 /dev/ttyS0’ to make it appear in the Serial Port Menu and you’ll have to add it to crontab (type in sudeo nano /etc/crontab, then add the line ‘ln - f /dev/ttyAMA0 /dev/ttyS0’ )to make it load up on boot.
Step2: Choose the correct serial port on the AduinoIDE
Step3: Do not hit the arrow icon to upload use Press CTRL+SHIFT+U instead of pressing upload.
Love the arduberry but this is a bit of a PITA to get to work along with having to unplug anything on pins 13-10. However I am sure you are working on it.