Considering using 4 pvc boards for dug well cover. Need a sealing layer to keep water out. A mastic might work too.
I wouldn't use EPDM and Pvc. EPDM is notoriously hard to bond and what few adhesives you can use aren't going to be made for use around potable water. I'd worry about chemicals that leech out of the adhesive contaminating the well.
I would stick to materials and adhesives that are known to be safe around potable water. PVC is safe for pipes but I don't know if PVc deck boards are. If you want to use PVC boards, you could use stainless sheet metal over them as a waterproof membrane. Stainless is not cheap but does hold up.