Hi Nathan
Im about to embark on a very similar project, its old imagery over an area that is now a dam and lake, so thanks very much for your write up. There is a couple of tips in there that will definitely save me some time.
I have also used Pix4D unconventionally for registering old hard copy plans (larger than A0) (far too big for us to scan) by hanging them on the wall and taking a series of photos with an SLR and using Pix4D to digitally put them back together. Worked quite well. The plans had grid lines from an old coordinate system on them so used the intersection of the grid lines as control points.
Cheers Simon