Actually thats a better water separator setup than the 6.9 had. Nothing wrong with your setup.

Only thing to do is swap the O rings around with different sizes until you get one that holds. Next time you have it apart, take a magnifier glass to the sealing surface of the O ring and look for any signs of a scratch or dirt that might be preventing a proper seal.

Other option is to take it a part, clean everything, and re install with a bit of oil resistant RTV sealant (permatex ultra black for example). Has to be perfectly clean and dry of fuel and solvent the sealant won't bond though.

I had a leak at the filter change prong on mine (which I don't use) and ended up just sealing it off with some RTV. That was a couple years ago and its still holding.