I have a Navio2 with Rpi 3. As I have random log problems, I had a try with Raspbian image on an USB drive.
My Rpi3 is patched to boot from USB,
Fresh Navio2 img is installed on the USB drive with Etcher,
/boot/cmdline.txt and /etc/fstab are edited for USB Boot.
ssh connection is fine, Ardupilot config is OK with emlidtool (no error with sensors before enabling arducopter).
UDP Mission Planner connection is ok but Navio is chasing Horizon around the planet. Even after calibrating Accelerometers and Compass, Horizon is still moving in the HUD.