I know it’s been a while since you first posted, but try these and see what happens, post another .bin log if you like
Update the CAN GPS firmware
Update the Arducopter version to latest stable
Connect to MissionPlanner, Initial Parameters, put in your battery info and accept all the battery-related settings it offers. Including:
BATT_FS_CRT_ACT,1
BATT_FS_LOW_ACT,2
I would highly recommend FENCE_ENABLE,1 since this is big, expensive and potentially dangerous.
You just have to wait for a good GPS 3D Fix and (wait a bit more) for Home to be set.
Harmonic Notch Filter is doing nothing, set this:
INS_HNTCH_REF,0.53
Also set this and let’s see what is going on:
INS_LOG_BAT_MASK,7
This will reduce the yaw severity a bit and might allow a bit better pitch/roll attitude control. Having these yaw P/I values too high can induce some yaw oscillation at arming. Changing these is not essential.
ATC_RAT_YAW_I 0.08
ATC_RAT_YAW_P 0.8
This should settle down the oscillations in Loiter:
PSC_POSXY_P 0.5
PSC_VELXY_D 0.25
PSC_VELXY_I 0.5
PSC_VELXY_P 1.0