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Tissue deformations due to cutting are tricky, and usually require pretty
heavy affine transformation (unless you photograph the block face, which
can't be used in this case). Derek Magee presented an elegant solution a
few years ago:
Magee D., Treanor D., and Quirke P., A New Image Registration algorithm
with application to 3D Histopathology *Proc. Microscopic Image Analysis
with Applications in Biology (MICCAI Workshop)*, 2008
I'm not sure about the availability of the algorithm, but you could contact
him directly via
http://www.comp.leeds.ac.uk/drm/
(where you'll also find the pdf of said paper).
There's many other approaches (e.g. Eric Bardinet et al.'s block matching
or Amelia Cifor/Tony Pridmore/Alain Pitiot's work), but again, I don't know
about algorithm availability - certainly no ImageJ plugins.