I'd go with the ping pong ball type check valves, as I think they are less susceptible from defeat from debris. I've heard stories of the duckbill type leaking because trapped debris kept them from sealing completely. However if you're leaving the boat in the water, you aren't too far from a "mode shift" from self-bailing to self-sinking!
I'd look at moving batteries, etc. to get some weight forward to get a little more self bailing margin!
I use the "vortex" type check valves, and I believe they work best in the vertical scuppers because it depends on the water pressure in the tube to collapse the glove finger. I use them when diving or fishing when I'm gonna have water on the deck anyway, because they allow it to drain off automatically. (Note: haven't tried the condom option, but I make them using Nitril gloves instead of vinyl or latex, as that material seems to be more durable!) However they don't seal perfectly. My waterline is about like yours, and if you're sitting or standing in the back of the boat, water will slowly seep in. When I'm cruising and want a dry deck, I use the rubber plugs and would use those and depend on bilge pump and a good battery if I left boat in water for a long period of time.
By the way, how do you like that E-Tec?