Thanks for confirming that changing the MOT_PWM_TYPE had no effect.
Leaving the AHRS_ORIENT is ok. This is more just a note (for myself and other devs) that the vehicle has a rare setup which means that it is more likely that we have a software bug that nobody has noticed before.
Re testing EKF2, using the latest beta would be good. thanks!
The new firmware: when switching to Loiter the shakes started immediately but after flying it a tad the shakes went away. I do see this from time to time when first taking off in Stabilize with new frames but fly for a bit and its gone but once and a blue moon but not in loiter like this.
I always keep my FC flat and never rotate the FC like it is currently add the fact that the compass is also rotated this could be the issue, this frame is intended to use Plane firmware FBWA and Qloiter. currently in Quad.