Update (in case anyone is having the same problem)

SurfVols should have skull on by default. The one I was working with did not (I inherited it from a previous lab member and there is something not right with it)

I regenerated the surface model from the anatomical from scratch using recon-all in Freesurfer, then used suma make spec hires to generate the SurfVol again. SurfVol now is correct and has a skull

Now that it has the skull the following alignment (below) works well

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# Copy surfvol to experimental folder
3dcopy $surface_dir/{$surf_subj_num}_{$subj_init}_SurfVol+orig \
$output_dir/rm.{$surf_subj_num}_{$subj_init}_SurfVol

# Zeropad SurfVol
3dZeropad -I 100 -S 100 -A 100 -P 100 -L 100 -R 100 \
-prefix rm.{$surf_subj_num}_{$subj_init}_SurfVol_padded \
rm.{$surf_subj_num}_{$subj_init}_SurfVol+orig

# Then open SurfVol it and nudge it towards the location of the anatomical

# Create a nudged surfvol in the experimental folder
3drotate -quintic -clipit -rotate 7.50I -4.33R 30.09A -ashift -15.71S -55.16L -20.99P \
-prefix rm.{$surf_subj_num}_{$subj_init}_SurfVol_padded_nudged rm.{$surf_subj_num}_{$subj_init}_SurfVol_padded+orig

# Make transformation matrix
cat_matvec 'rm.'{$surf_subj_num}'_'{$subj_init}'_SurfVol_padded_nudged+orig::ROTATE_MATVEC_000000' -I > XFORM0.1D

# ======================= surf (map data to surface) =======================
# map EPI data to the surface domain

# align the surface anatomy with the current experiment anatomy
@SUMA_AlignToExperiment \
-init_xform XFORM0.1D \
-surf_anat rm.{$surf_subj_num}_{$subj_init}_SurfVol_padded+orig \
-exp_anat $exp_anat \
-wd \
-prefix {$subj}_SurfVol_Alnd_Exp