Hi, George-

Well, indeed some of those options like -giant_move might help. Skullstripping your brain before using afni_proc.py might also help (for example, how does your skullstripped brain look in the output of afni_proc.py? If there is lots of extraneous stuff or parts missing, that could be bad for alignment). If your EPI and anatomical dsets don't have a lot of overlap initially, as well, then putting the center of mass would be a good start, even without the full giant_move.

Adjusting the cost function to include some others might help, for example use the option:
-align_opts_aea -cost lpc+ZZ -giant_move

--pt