Oblique slices are not going to work well in AFNI.

There are several other issues I should probably address in
your post, but it mostly comes down to that.

1. You are reading it in using the "3D:" mechanism, so the
information you give it on the command line is the only information
AFNI has about the position, orientation, and scale of the input
image. You are not giving AFNI any information about location,
or actually you are implicitly saying that it is centered about zero.
If this is a file format that AFNI understands, it's possibly that
AFNI could extract some of that information from the file itself,
but it looks like you're probably using data in a custom format
for the surface coil data, so that's unlikely.

2. Even if you gave AFNI correct position information, AFNI
doesn't maintain information about obliqueness, so you would
either have to view it in your current ugly rotation, or rotate
your functional data using obliqueness information from your
scanner, and/or:

3. You probably are referring to the "ugliness" in the fact that
your functional data don't overlay your structural scans very
well. The best thing to do is to rotate your structurals to match
your functionals, based again on that information from your
scanner about the oblique angles of acquisition. You will also
need to offset your functional data from the center, based
again on information you'll have to get from your scanner,
in order to get the proper relative position. Or you can manually
nudge and rotate the functionals to match the anatomicals,
using some plugin....probably Nudge Dataset. There are others
who know more about this than I.

But to help you in any more detail, we'll need more information
about your oblique datasets, specifically if they are in a
data file format about which AFNI is savvy. Or, you'll need
to get information about the relative position and orientation
of your anats and funcs from some other source, like good
records kept by whomever made the scans. Good luck!

rich