Thanks guys, I'm really glad I decided to post to the message board instead of spending 3 more hours poking and hoping.
Rick's solution with 3dTcat was the simplest and worked like a charm. Plus I was able to do it all on existing nifti images without going back to afni ones.
So, if anyone ever has nifti - abuc images that they would like to warp with ANTS, I did it this way:
3dTcat -prefix tmp_ts.nii.gz orig_abuc.nii.gz
WarpTimeSeriesImageMultiTransform 4 tmp_ts.nii.gz mni_ts.nii.gz -R mni_2mm.nii.gz orthoanat_to_mni_SYNWarp.nii.gz \
orthoanat_to_mni_SYNAffine.txt
3drefit -space MNI mni_ts.nii.gz
rm tmp_ts.nii.gz
