There are lots of options here, but what makes most sense depends on what your goals are.
If you are going to put these datasets into afni_proc.py, I would try to avoid regridding either, but most importantly not the EPI (regridding the anatomical is probably less of a concern).
If you want to get rid of obliquity without regridding *and* have the dsets be pretty well aligned, you could do the following on each to remove the obliquity information while preserving the location of the coordinate origin in the dset, where (x,y,z)=(0,0,0):
3dcopy DSET_ORIG tmp
3drefit -oblique_recenter tmp+orig
3drefit -deoblique tmp+orig
3dcopy tmp+orig DSET_NEW
The dsets should be quite close to still aligned, if there wasn't a huge amount of relative obliquity between them originally.
Note the use of 3dcopy initially, because 3drefit changes header information. And also note that "tmp*" should be a BRIK/HEAD file, as here.
--pt