Hi Paul,
Thanks a lot for your response!

Actually both the preprocessing and the apqc_make_tcsh.py command are being run using the same version of AFNI from 2 years ago (it's the one we have installed on our clusters). And the results folder does have a .json file in it. This is what is in that json file:

   "afni_package": "linux_openmp_64", 
   "afni_ver": "AFNI_19.2.01", 
   "align_anat": "sub-002_al_keep+orig.HEAD", 
   "censor_dset": "censor_sub-002_combined_2.1D", 
   "cormat_warn_dset": "out.cormat_warn.txt", 
   "df_info_dset": "out.df_info.txt", 
   "enorm_dset": "motion_sub-002_enorm.1D", 
   "errts_dset": "errts.sub-002.tproject+tlrc.HEAD", 
   "final_anat": "anat_final.sub-002+tlrc.HEAD", 
   "final_epi_dset": "final_epi_vr_base_min_outlier+tlrc.HEAD", 
   "final_view": "tlrc", 
   "flip_check_dset": "aea_checkflip_results.txt", 
   "flip_guess": "NO_FLIP", 
   "gcor_dset": "out.gcor.1D", 
   "have_radcor_dirs": "yes", 
   "mask_corr_dset": "out.mask_ae_dice.txt", 
   "mask_dset": "mask_epi_anat.sub-002+tlrc.HEAD", 
   "mot_limit": 0.3, 
   "motion_dset": "dfile_rall.1D", 
   "name": "user variables", 
   "nt_applied": 346, 
   "nt_orig": 348, 
   "num_stim": 0, 
   "out_limit": 0.05, 
   "outlier_dset": "outcount_rall.1D", 
   "pre_ss_warn_dset": "out.pre_ss_warn.txt", 
   "rm_trs": 4, 
   "ss_review_dset": "out.ss_review.sub-002.txt", 
   "stats_dset": "NO_STATS", 
   "subj": "sub-002", 
   "sum_ideal": "sum_baseline.1D", 
   "tcat_dset": "pb00.sub-002.r01.tcat+orig.HEAD", 
   "template": "MNI152_2009_template_SSW.nii.gz", 
   "tr": 2.0, 
   "tsnr_dset": "TSNR.sub-002+tlrc.HEAD", 
   "volreg_dset": "pb02.sub-002.r01.volreg+tlrc.HEAD", 
   "vr_base_dset": "vr_base_min_outlier+orig.HEAD", 
   "xmat_regress": "X.xmat.1D", 
   "xmat_uncensored": "X.nocensor.xmat.1D"

I tried running the steps from your post above and everything else seems to run successfully, but I'm still getting same error for the apqc_make_tcsh.py command (with the exception that before I ran those steps in your message, it said it had 39 files for QC-ing!):
++ Found 40 files for QCing.
** ERROR: radcor number of ulays (0) doesn't match number of olays (6)

Side note: A friend of mine (Jenna from UWM) is doing the same thing on her data on the cluster using the same AFNI version, i.e., running afni_proc.py and then separately running apqc_make_tcsh.py commands- and she was able to generate the HTML files. She has one run of resting state data, and her afni_proc.py command is almost identical to Example 11 on the afni_proc help page. Haha! Not sure if that's helpful for you to know, but that might suggest it has something to do with my data?
Thank you,
Mrinmayi