Hi julesmalcomson
I highly recommend you to create one perfect alignment (on shooting start) with something like mock-up head with plenty of non-uniform patterns like newspaper pattern. Then set scale orientation etc.
And use XMP workflow for transferring the alignment to other data, so you do not need to realign and will not get into trouble.
Have you seen the XMP workflow or do you need my assistance? Can you prepare a good alignment dataset, so that I can instruct you further?