You shouldnt need to specifically “tune EKF2”. It’s behaviour and default settings have been worked out over years and millions of flights (not to mention all the theory and maths). This learning and experience now carries over into EKF3. If you just want your multirotor to fly properly then it’s a well-understood process with plenty of documentation and examples of the process.
I can only assume you are worried about this Altitude versus Desired Altitude problem. It’s the only strange thing I could see in the log. Please say of there is some other specific issue.
You’ve got quite a few warning messages all related to position
I would look at reducing Z axis vibrations before flying more. Although not in the official danger zone they are getting into that grey area of “no one is sure what will happen” and clearly you have some issues going on there.
Also try GPS_GNSS_MODE,65 to see if that helps with the GPS glitches. A combination of an unsteady stream of GPS data and poor IMU position (vibrations) will trigger those GPS glitch messages.
Any reason you have every flight mode set to RTL ? What if you need to take control in Stabilize mode or even AltHold or Loiter?
You should definitely set these:
Your MOT_THST_EXPO looks wrong and probably should be around 0.75 to 0.8
Just asking, but what’s with Bat and BAT2 having different scales? You should fix BAT2 or disable it.
After all that, your aircraft is quite responsive and relatively stable. You should be able to set up the Harmonic Notch filter and run Autotune once the vibration problem is fixed.
Next time just try some gentle hovering and movements, ascents and descents. No need to test to absolute limits at the fastest rates possible, that just hides problems amongst the data. Wait till everything is just right before that sort of testing.