Well Ellis is right, I was basically just looking for tips on getting the 2 planes aligned. In the end I just marked the extreme L & R edges of the field of view on the wall and measured the distance from each edge to the edge of the lens hood. Spirit level sort of deals with vertical alignment.
For the purpose of alignment, I keep a mirror tile (they come in sets of 10, from a local DIY home decoration store) in my bag. It's very easy to get alignment that way because you can see exactly what you're doing.
I don't think the Canon 100 particularly suffers from curvature of field but I will try what you suggest when I get round to testing the Zeiss 28/2 which I think maybe does.
The Canon 100mm maco lens(es) is (are) quite good. However, at high magnification factors your DOF is verry narrow, which leaves little room for error, especially when used with wide apertures. I recently helped a fellow photographer with deciding whether his new lens was good, and it had 1 corner that was significantly less detailed compared to the other 3. It remained so after repeating the experiment (to rule out a glitch in technique like in focusing or camera shake), so the lens was returned and exchanged for another copy, which performed very well in all corners and in the center.
A 28/2 has much more DOF at common shooting distances than a 100/2.8, but it still helps to focus individually on each corner.
However it is a bit difficult to focus into the corner when using LV , magnifying the central section, without moving the tripod head to focus and recompose, which can in itself introduce inaccuracies at close distances. I suppose I'd have to keep LV at full frame and use the loupe in the corner.
Using 10x zoom in LV, and shifting that LCD preview area to a corner for manual focusing (or contrast detect focusing) is the way to do it.
Cheers,
Bart