You should do slice timing correction with 3dTshift before running 3dWarp on an EPI dataset. Make sure the result overlay well in the AFNI GUI to be sure you haven't clipped off a big chunk of the data. Also you can run 3dToutcount before the 3dWarp. The results should not change very much, I would think, by the transformation.
Consider using align_epi_anat.py to align the EPI dataset to the anatomical dataset. It will include the slice timing correction and the deobliquing and align the EPI data to the anatomical dataset too.