Hi Paul,
I don't use the option of "-volreg_align_e2a" because there is not anatomical data involved here. My afni_proc.py options are as simple as this:
-blocks tshift volreg mask combine \
-dsets_me_run ./data/rest_echo-?.nii.gz \
-echo_times 15 37.14 59.28 \
-reg_echo 2 \
-volreg_align_to MIN_OUTLIER \
-combine_method tedana \