Hello Paul,
Usually it is necessary to have at least three reference points for georeferencing, it includes camera locations and marker (GCPs) locations, providing that cameras are aligned and each marker has at least two projections on the images from aligned image subset.
The coordinates of the camera locations should represent the camera center at the moment the image were taken. As for the yaw, pitch, roll angles - currently PhotoScan assumes that camera is fixed under the aircraft in such way: when the aircraft is flying to the North and East is by the right wing (Yaw, pitch and roll are all zeros), the camera is pointing vertically down and the image axis bottom -> top direction is pointing to the North, whereas left -> right vector is pointing to the right wing. In case the camera mount is different, but yaw, pitch, roll angles apply to the aircraft as described, it is necessary to use the GPS/INS offset values in the Camera Calibration window.
Note that gimbal angles are not supported (varying angle offset for each camera position), so in such case pre-processing correction of the orientation angles should be used. Or angles should be ignored and not loaded to Reference pane.
As for the issue with the stereopair itself, there could be several reasons, for example, very short stereobase distance compared to the distance to the area of interest.
If you know the camera calibration parameters precisely, you can input them to the Camera Calibration window and use Fix Calibration flag to disable automatic distortion parameters refinement.