There is a big problem here:
Your wiring color code is disturbing (receiver to Navio2). Verify that signal line from receiver (not ground) is well on the top line of Navio2 pins.
ESC plugs are reversed (top to bottom). Signal is orange, ground is brown.
Normal, you cannot use mission planner to update your arducopter software.
When you will be OK with 3.6.5, have a look at https://community.emlid.com/t/navio2-arducopter-upgrade/10743
There were some changes in the Emlid file structure but you can edit some lines and do it.
Marc