Thank you for your response!
I did as you said and found the file in the afni_proc.py resulting script.
For anyone else who might be in the same position, I used "anatQQ.s001.aff12.1D", and my 3dNwarpApply looked like the following:
cat_matvec -ONELINE \
anatQQ.s001.aff12.1D \
anatSS.s001_al_junk_mat.aff12.1D -I \
mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D
3dNwarpApply -master anatQQ.s001+tlrc -dxyz 3 \
-source pb01.$subj.r$run.tshift+orig \
-nwarp "anatQQ.s001_WARP.nii mat.r$run.warp.aff12.1D" \
-prefix rm.epi.nomask.r$run
Thanks again for the help!