Thank you for your responses on this, I've nearly finished aligning the chuncks.
stihl your idea seems the best, is there any online info on how to do this, I looked in the photoscan manual but information is vague.
mwillis, yes there are a fair few archaeologist working with photogrammetry, some using it better than others. As for using google earth for elevation points, I would be strongly against it, Google Earth, or any similr app, is extremely inaccurate, the georefereced images can have great spatial errors, in some cases things have been 100m+ off.
dcm39, we seem to be in the same boat! The GPS guy took z coordinates of my gcps but discarded the ones for the site grid, so I have a few known height points (10) and 30 known xy points without a z, surely this could be something photoscan could resolve? e.g. what is the elevation a point xy if z is not specified?
sakaic, I'm wanting a full 3D model, I will be creating an orthophoto for 2D GIS but I will also explore the 3D GIS possibilities.
Thank you all, if anyone else has a solution I am eager to hear
Gary