Hello Łukasz Prokop,
The vehicle altitude and climb rate estimation does not add up. The climb rate is almost never around zero during the whole flight. Even at the time when altitude is constant. You can better see this discrepancy at EKF estimation log.
If I am not misreading, IMU0 is the primary core during the whole flight. It can clearly be seen that vertical position and speed estimation are not kinematically consistent with each other. Meaning, for constant altitude estimate, the vertical speed estimate should be around zero. This is only the case for the core that uses the IMU1.
The barometer measurement seems to drift a lot. There is a nearly 20 degrees Celcius temperature and 7.5 meter altitude change for 3 minutes of flight. Is this an original pixhawk or clone? Where is the flight controller located inside the frame?
Seeing that this vehicle uses 12S battery and I don’t have too much experience with a vehicle this big. I will step aside for someone else to comment on your vibration level.