Daniel I used align_epi_anat.py with the final output of functional images from afni_proc.py before deconvolution/regression and the alignment results seem to be very good. When using afni_proc.py, 3dcopy is importing my .nii files immediately into +tlrc automatically. So it won't tlrc warp within afni_proc.py.
Rick I'm going to follow your suggestion and run 3dcopy, 3drefit -view, 3dunifize, and @Align_centers before afni_proc.py to see the automatic warp/alignment produced as I want to avoid too much additional blur.
Thank you both for the help.