Hi Richard, just starting to look at your logs now.
I notice it is running a firmware from 1st March. When working with such bleeding edge features in ArduPilot it is best to test the latest firmware. Once support for tailsitters matures then using the stable releases would be recommended. I suspect you are not familiar with the GCS interface for getting the latest builds. In MissionPlanner firmware load you can use control-Q to get the latest firmware. Or download from here:
This firmware version does support tailsitters, but is missing some features and the logging doesn't take account of the 90 degree AHRS view change when hovering, so logs are a bit harder to analyser.
I notice you turned off arming checks with ARMING_CHECK=0. Sometimes there are good reasons for that, but in this case I think you would have had some important warnings. In particular your GPS seems quite unhappy in 44.BIN. In 45.BIN it is quite a bit better. In 44.BIN I see high EKF position innovations (see NKF3.IPN NKF3.IPE in the log for example). That means the accelerometers and the GPS velocity were inconsistent. I've suggested above (after your flight, sorry!) that switching to EKF3 would be a good idea to ensure that accel biases are learnt on all axes.
The the QHOVER part in 45.BIN it seems to be holding height reasonably, but not great. The throttle is varying quite a lot more than it should for a steady hover. It is staying within about 20cm.
At the end of the hover the throttle went up a lot but the aircraft didn't climb. Did it just run low on battery? Battery monitoring is disabled so I can't tell easily. The board voltage (POWR.Vcc) is varying a lot more than it really should. It should stay close to 5V, but I can see it get down to 4.4V at times. How are you powering the board?
Your Q_A_RAT_YAW* gains are setup for a multicopter (see comments in discussion above). Setting the I up equal to P will help. You probably also need some FF gain. I'd suggest 0.25 to start with on roll, pitch and yaw axes. Yaw control looks quite weak.
It is a bit hard to analyse the overall performance of your PIDs with the firmware from early March as it suffers from gimbal lock. Could you try another flight with the latest firmware, and the following changes:
also try with ARMING_CHECK=1 and see what it complains about (if anything!)
I'd also suggest you push up MIXING_GAIN. It is currently 0.5. I think 0.8 to 1.0 is right for tailsitters. That will effectively raise your gains though, so you may get oscillations and need to scale them back.
I think that is enough changes for the next flight. I can look at the results and iterate from there.