@mijarven here are some of the interesting details I see in your log file:
at 1:44 there is a "ubx msg 0x0104 invalid len 64530" warning. This could be an indication of corrupt data over the GPS serial line. Check your wiring.
The GPS data stops completely 5 times, again this indicates you probably have some wiring problem. Also, for some reason the EKF only shows 2 logged GPS problem events which seems like an unrelated PX4 problem, i.e. it should be logging a message anytime GPS data disappears I would think...? (@dagar ? @Paul_Riseborough ? ):
your airspeed data is dropping in and out constantly. Probably a wiring problem again. I don't know why there aren't any logged messages about this, should there be? (@dagar)
I'm guessing having the airspeed drop in and out is causing the controller to do bad things with throttle, which is also hammering on and off:
overall, check your whole avionics installation.