While I don't own a 6.7 diesel, I was talking with the service manager at the dealer where I live because of my interest in purchasing one and was talking to him about my fear of the fuel system's oversensitive issues, specifically regarding moisture. I told him that I had read about people putting aftermarket spin on filters/water separators on their trucks and when they'd take them in for warranty work, the dealerships would shun them away and refuse to work on it. Turns out, that's illegal.
Our discussion basically led to the fact, that if you put a second, third or even a fourth filter on of your choice, that it is ILLEGAL for them to turn you away. All you're doing in cleaning the fuel more so than what the OEM system is doing. Basically what it boils down to is how much time you have (to fight the issue and time without your vehicle) and how much money you have, which could later be recouped from Ford.
He specifically told me that Ford's track record with lawsuits over this type of BS customer service is not a very good one. I was informed that Ford has lost EVERY SINGLE lawsuit in that case and here's why;
When you take you truck in and tell them that your truck's fuel system is acting up. They look at it and see that you have a NAPA 3405 12 micron water separator and NAPA 3528 2 micron fuel filter (incidentally the very same setup I have on my 6.0L) and push you away. Instead of you having to prove that the filters weren't the cause of the problem, for the purposes of lawsuits, Ford has to prove it was. That's extremely difficult to do, especially when they pull that filter off and see how clean and clear it was and test it for water and see there is none. That's info worth knowing. So, you can take it for what's it worth and use this advice to help you out or not, I'm just presenting the info for all you 6.7 gurus. I now kinda want to get one after all.
Oh, as for my filter set up for those curious, I changed both of them today and I could have poured them in a clear plastic bottle and sold it as water, that's how clean that stuff was. Again, good info to know about warranties and related problems with Ford and it boils down to this;
They have to prove it caused the problem, not you proving it didn't.
Hope this helps folks!