Howdy-
Stepping back a pace, what kinds of images are you aligning, and what AFNI functions are you using for this?
There is AFNI functionality for doing manual adjustment (the "nudge"ing plug-in: open AFNI -> click "Define Datamode", a button in the middle, then click "Plugins" in the lower right of the panel that opens, and select "Nudge Dataset" in then menu that opens), as well as 3drotate on the commandline, which might be useful.
However, it might be better (both for the current alignments and in the longer term) to sort out alignment on the command line.
-pt