(1) I have no idea what FSL version correpsonds to the older ANALYZE-7.5 files and what version to the newer NIfTI-1.1 files.

(2) The -fsl_matvec option is just to interchange x=-x and y=-y since the AFNI internal coordinate system follows the DICOM ordering, while FSL and SPM follow the 'neuroscience' orientation.

(3) I guess that the .mat files you are talking about are the ijk-to-xyz transformations. At present, AFNI doesn't have much to deal with these. What do you want to do with the catenated transformation, anyhoo? I mean exactly - what program(s) will it be put into, and applied to data in what format?