It looks like you’ve got a bit of weight imbalance, motor outputs are not as consistent as they could be - but not a show-stopper.
Probably take the PID tuning off channel 6 unless you’re really good and familiar with using that.
Change
ATC_INPUT_TC,0.2
to smooth out your RC control a bit, you can make it higher too if you like, 0.22 or 0.25.
I’m not sure what BATT2 is monitoring but the voltages and current are totally different to BATT(1)
And this is not right:
BATT2_LOW_VOLT,10.5
Set these if you are using 12 cell LiPo for BATT(1)
BATT_ARM_VOLT,44.3
BATT_CRT_VOLT,42
BATT_LOW_VOLT,43.2
BATT_FS_CRT_ACT,1
BATT_FS_LOW_ACT,2
You could probably increase ATC_ACCEL_Y_MAX up to 9000, or at least 4000
You ATC_ACCEL_P_MAX and ATC_ACCEL_R_MAX are quite different - I guess the craft or payload is not symmetrical in every direction? That can also happen if running autotune in the wind.
If it is symmetrical then you can set them the same at about 20000 - in fact I would since your Roll response is not as good as your Pitch response.
I’d set these:
ATC_RAT_PIT_FLTD,8.5
ATC_RAT_PIT_FLTT,8.5
ATC_RAT_RLL_FLTD,8.5
ATC_RAT_RLL_FLTT,8.5
ATC_RAT_YAW_FLTE,2
ATC_RAT_YAW_FLTT,8.5
INS_GYRO_FILTER,17
And give it another test flight. Lets see the .bin log from that.
Also I wondered about the PIDs since the Pitch and Roll responses are not ideal. Might be an idea to start over with them, maybe something basic like:
ATC_RAT_RLL_P,0.1
ATC_RAT_RLL_I,0.1
ATC_RAT_RLL_D,0.005
ATC_RAT_PIT_P,0.1
ATC_RAT_PIT_I,0.1
ATC_RAT_PIT_D,0.005
See if anything needs manually adjusting because of oscillations or hot motors and so on, then move on to Autotune. Yet another .bin log 