Hi Joseph
When a PID control is not stable I usually try to set the I-gain to zero. I therefore recommend to reduce AUTO_THROTTLE_IGAIN further or set to zero. And your P-gains might be further enlarged.
When tuning Paparazzi it is important to tune AUTO1 well before approaching AUTO2. The plane must fly stable in AUTO1 (no oscillations) and react quickly to control inputs (no sluggish behaviour). Does your plane do so?
I hope that helps. Unfortunately I cannot look at your log right now due to system problems on my side for in depth analysis.