So I've done some more testing, and the attitude control looks to be working pretty well, and I did some RTH tests which went without problem. I thought that RTH would always return to the altitude it was first set at, but it appears it just returns to the home position at the current altitude.
My position hold looks to be circling a little (~1M diameter) at low altitude (1-2M alt) but holds better up higher. Not sure what's causing that.
Looks like my latest log might be corrupt too. When I select the log file, none of the boxes on the right are prefixed by LOG_ and a bunch are missing. I can't show any curves for any that are selected. Selecting an older log file everything looks normal.