I have had some success copying/modifying an afni_proc.py script to grab the 1) pre-processed files from one "results" directory; 2) the motion estimates (from 3dvolreg); 3) the anatomic; and 4) the stim files. You could then use the modified afni_proc.py script to quickly generate a script doing just the masking (I think this was necessary to get 3dClustSim to run) and regression. Example below, "mystudy" was the first run through, and mystudyTENT is the second run through.
afni_proc.py -subj_id $aSub -script afni_$aSub_mystudyTENT.tcsh -out_dir $aSub.mystudyTENT \
-dsets $aSub.mystudy/*pb03*.HEAD \
-blocks mask regress \
-copy_files $aSub.mystudy/dfile_rall.1D $aSub.mystudy/*anat_final* \
-regress_stim_times $aSub.mystudy/stimuli/times* \
-regress_stim_labels c1 c2 c3 c4 \
-regress_local_times \
-regress_motion_file $aSub.mystudy/dfile_rall.1D \
-regress_basis 'TENT(-4,14,10)' \
-regress_censor_outliers 0.1 \
-regress_censor_motion 0.3 \
-regress_est_blur_epits \
-regress_est_blur_errts \
-regress_opts_3dD \
-num_glt 11 \
-gltsym 'SYM: +c1[5..8] -c1[0..3]' -glt_label 1 'print' \
... \
-execute