Hello Doszpot,
I think that you can follow this approach:
- using Rotate Object tool properly orient the reconstructed model in the coordinate system according to the axis shown in the bottom-right corner of the Model view,
- create markers in the Model view in the points of interest (later you can adjust their projections on the individual images in Photo view mode), if markers are already created, then create the new markers next to them and copy the values from Source values tab of the Reference pane for these newly created markers,
- modify Z values for markers according to your measurements,
- use Set Accuracy option for the markers in the Reference pane to define very low accuracy of XY and adequate accuracy for Z, for example: 1000/0.5 would mean that XY accuracy will be 1 km and Z accuracy - 50 cm. Then press Update button on the Reference pane to apply the referencing information (you may need to check on the markers in the Reference pane first).