Couldnt download that log, it wants a sign-in
We can see tests without a payload, and low vibrations, then tests that must be with a payload (higher motor outputs) and there is excessive vibrations.
There is still a physical problem causing this, and it seems to be with the frame or parts because the copter doesnt appear to be bouncing up and down (altitude) or oscillating wildly (even though attitude control could be much better).
Have you got an updated photo of inside the flight controller box?
What is the payload and how is it attached?
Set these parameters which you will need anyway:
INS_ACCEL_FILTER,10
INS_GYRO_FILTER,20
INS_LOG_BAT_MASK,1
INS_LOG_BAT_OPT,4
LOG_BITMASK,180222
BATT_ARM_VOLT,44.30
BATT_CRT_VOLT,42.00
BATT_LOW_VOLT,43.20
BATT_FS_CRT_ACT,1
BATT_FS_LOW_ACT,2
MOT_BAT_VOLT_MAX,50.40
MOT_BAT_VOLT_MIN,39.60
Why not put back these, which I thought were working OK perviously?
ATC_ANG_PIT_P,5
ATC_ANG_RLL_P,5
ATC_INPUT_TC,0.22
ATC_RAT_PIT_D,0.0028
ATC_RAT_PIT_I,0.17
ATC_RAT_PIT_P,0.17
ATC_RAT_RLL_D,0.0028
ATC_RAT_RLL_I,0.17
ATC_RAT_RLL_P,0.17
ATC_RAT_YAW_I,0.05
ATC_RAT_YAW_P,0.5
and at least get it flying OK without a payload. Hopefully you can fix the vibration issue before another flight attempt (or it will never fly properly 
)