It's hard to tell with only the script. The skullstripping may be part of the problem you're running into, or your anatomical data may have artifacts that limit the alignment. A couple recommendations:
1. Template - use one of the more modern templates instead like the MNI_2009c template. We provide a unifized version you can use with @SSwarper. That program will do the skull stripping for you too.
2. afni_proc.py - use this program to generate a script. It can take the output from @SSwarper as part of its input.
