I think Stainless Steel screws under epoxy should be fine - but i would never remove the Oxygen on something critical as for Stainless Steel to...
If the Stainless Rust or Tea-staining is superficial you can clean it off pretty easily with a Phosphoric based cleaner, something like this:...
If you put in Stainless keel Bolts (which is a good idea) be careful of the grade as 316 won't be good enough, might need to get Duplex bolts...