Periodically, the question is asked on the Zen Cart forum, “how can I set the Zen Cart Free Shipping threshold based on the Total AFTER all discounts and coupons have been applied?”
This can be done but there are a lot of variables involved. (If it was a simple mod, I’d package it up as a simple mod!) So I offer it as a service. It’s called Free Shipping Recalculation. It recomputes your free shipping threshold based on the subtotal after discounts.
Free Shipping Recalculation works, whether you are using Admin->Modules->Shipping->Free Shipping Options or Admin->Modules->Order Totals>Shipping to set your free shipping threshold.