Thank you for the log file. Here are my initial observations. (I can continue looking at it)
The target detection is consistent, indicated by smooth 'pX/pY' curves. That is good, since we can focus on analyzing the controls.
I would strongly recommend switching to the latest ArduCopter firmware. This particular flight was conducted with V3.4.6. My main concern is that some of the older firmwares use a newly-developed EKF for estimations in the precision landing controls. I have observed that the precision landing EKF has produced mixed results: great in some cases, and poor in some cases.
In the latest firmwares, you can disable the precision landing EKF by setting the parameter PLND_EST_TYPE = 0 (RawSensor). This parameter does not exist in V3.4.6. The RawSensor estimation type seems to provide more consistent results for a broader range of copter setups.
Also, is there a particular landing you would like for me to analyze? (e.g., "landing prior to 1 minute mark of log") I am definitely not the expert on the precision landing EKF, but I am happy to make an attempt.
My primary suggestion is to switch to the latest firmware and set PLND_EST_TYPE = 0.