Overall, I would probably let afni_proc.py handle all this. If you put the exact afni_proc.py command you used, then we can advise. The obliquity that you are working to remove is used to align the data and included in the transformations. The EPI output will be put onto the same grid as the anatomical but with a reduced resolution. One important advantage is the data has only one interpolation.

With a 3dWarp transformation, you will get at least one more interpolation, and consequently, smoother data. It will still work, but you would just make the gridset option the output from the first run. If, on the other hand, you remove the obliquity information from the header with 3drefit, then you would add "-giant_move" to your "-align_opts_aea" in your afni_proc.py command.