Okay!
So I am trying out more things with the align_epi_anat.py script. I have tried 3dcopying the anatomy files from /opt/afni/ to my working directory. I have also tried adding -cost lpa (which supposedly estimates transforms better when going from anatomy to anatomy).
It's running now and the result is... "Finished alignment successfully"!!!
Great, thank you so much for the help and all the hard work you guys must have put into afni, documentation, and monitoring this message board! We really appreciate it.
Best,
Kirk