@sjweaver Thanks for trying my program! I guess I missed the other thread back then. I just updated the csparc2star.py tutorial on the pyem github wiki. The most up-to-date program and documentation can always be found in that repository.
At the end of the new tutorial, there are some detailed notes about why the results may not be as you expect. Let me know if you think something is missing - I suspect your issue is related to one (or more) of the suggestions there.