I think we need to make some modifications to align_epi_anat.py's functions regarding partial-coverage. So for now, I would recommend using 3dAllineate directly with the options specified.
For the nudge, I would go ahead and use the plugin, followed by 3dAllineate to do a quick alignment to get a rigid alignment (-warp shirt_rotate), and use cat_matvec to concatenate your two transforms (nudge + partial-coverage to anatomical). That's similar to what the -pre_matrix does and would potentially reduce interpolation. That said, you may also be able to eyeball the nudge and then use 3drefit to move the origin to get things close into place.