I'm in the same situation with a 1-acre pond. The main difference is that I have a lot of sandstone and sandy loam soil. IMHO, the only way to seal is to use a significant clay liner (2ft thick or more) that covers the rock over and above the water line or, as you mentioned, a synthetic EPDM liner. I've spent > $100k on rebuilding dam 3 times, special polymer coagulants, and attempting to stay head of leakage by pumping in more water than I lose. None of it worked, and was an incredible waste of time, energy and money.
I will be using an EPDM liner when my budget allows. When installed properly, it's the only 99% leak-free water retention system. That means a liner covering the entire pond and tucked in 2-4ft past the top of the pond edge, well above the water line.
