I have the same problem and need to evaluate data with ascending slice order. Unfortunately, both solutions are problematic. If I apply the hack, for which I added "slice_timing=2;" in qa_slomoco.m and read_motion_newslicealg.m as well as  "slice_acq_order=2;" in read_slicemocoxy_AFNI_files_auto.m, slomoco stops at a point of the processing with the following message:

Wait, script starting...

That seems to be a message from slicemoco_newalgorithm.sh, but I do not really understand why it occurs at all.
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In order to apply the version which you suggested first, the following replacement was carried out in read_motion_newslicealg.m:

mocoparams1=textread(sprintf('%s.0000.1D',filestr),'','headerlines',1);

replaced by

mocoparams1=textread(sprintf('%s.0000.1D',filestr),'','headerlines',1,$SLOMOCO_SLICE_ORDER);

If I proceed in this way the script stops without finishing the image processing.