I have a 2012 Dyna Super Glide I'm upgrading to a stage 3 kit and a CNC ported Head I found a base calibration for the Stage 3 upgrade but I don't know how to add the CNC head to the Calibration. Thank you.

 

Sounds that you might need to have a look at the stage IV configurations, CNC ported heads will be included there. Apart from that you will need to further tune it, the selected map is just a base map.