The align_epi_anat.py script should be able to get around the slice timing corrected dataset with just the warning, but you can turn that off with -tshift off. The problem here is that the median option for epi_base does not work with the child_epi dataset option by itself. You can, however, do this instead

align_epi_anat.py -anat anat+orig -epi epi_r0+orig -epi_base median \
-volreg_base 4 -suffix _al2med -child_epi epi_r*.HEAD

Normally the same base is used as the reference for volume registration (motion correction) of the epi dataset and for the alignment of the anatomical dataset to the epi dataset. So selecting just "-epi_base 5", for instance, selects sub-brick 5 of the first epi dataset for both volume registration and alignment. But they do not have to be the same sub-brick. Both the epi_base and volreg_base options allow numbered sub-bricks, mean, median or max. For most alignments though, a specific sub-brick is all that is necessary, i.e. "-epi_base nn".