Polyester doesn't bond well to epoxy. You can peel polyester-wetted fiberglass off of epoxy by hand. If you Google "System 3 Epoxy", they have a free downloadable handbook on their website that'll be very helpful in describing how to finish the transom, tie it into the stringers, build a deck, etc.
You can make individual parts with polyester and then use epoxy to bond it to the hull. For instance, you can use polyester to add fiberglass skins to foam core, then use epoxy to fiberglass those pieces to the hull. On a boat that size, you probably won't use enough resin to save much by mixing types.
You also don't have to stick with West System. The biggest advantage it has over other epoxies is mostly in it's ability to lighten your wallet. Once the epoxy is cured (a few days), you'll only be mechanically bonding to the existing work, so it doesn't matter if you change to Raka, System 3, etc.
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