Hi @Graphical,
Let's rule out the obvious stuff first. Have you tried running the calibrator on another computer (either Mac or PC, doesn't matter) to make sure it works there?
Of course you don't crop during editing (with photobooks OR regular prints). Edit the whole photo at its full size as usual, then only resize and sharpen when you're ready for the book.
As long as the focus was perfect, and you don't need to crop them for composition, you'll be fine.
But you'll need to be utterly ruthless when culling for focus. If it's remotely soft, it's gone.
Now's the time to take the Bridge Class.
What I've found is that you need to vary the blend mode of the Solid Color layers for various purposes. Sometimes "Color", sometimes "Multiply", sometimes "Soft Light" etc.
Yes, I know, I already told you. You do it at 100%, then lower the opacity of the whole layer. Or, in the Masks panel, lower the Density slider of the mask.
I need you to tell me exactly what you're trying to achieve with a specific photo.