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Not sure that this is the most efficient method, but you might consider adding to the approach of the script to fetch the folder structure (you can reference previous threads on this here, here, or even here, etc).
This way, you can not only recreate your folder structure (which - from the sound of it - contains numerous folders), but by reapplying the explicit permissions you gained from your original script, the permissions will inherit and you should have your entire folder structure recreated - with permissions - programmatically.