As evidenced by all of the differing opinions, I'd contact the manufacturer of the waders (even though the OP probably negated any warranty by adding the zipper) and ask them what THEY recommend.
That being said, to do it correctly it is a two step process:
Wash first then apply a durable water resistant (DWR) treatment to the fabric to help it shed water like they did when new.
A DWR treatment is applied to all waders during the manufacturing process so at minimum a reapplication occasionally by the owner will NOT stop leaks but will aid in the overall water repellancy of the fabric.
BTW - DWR products are sold as DWR products for fabrics and are not just your garden variety waterproofing stuff.
Good luck and be careful not to pi$$ all over your clean waders trying out your new zipper.