I'm flat footed too and have been fitted with New Balance 855 at factory store in San Francisco a few years ago. This was when I was running marathons, relays, trails, and my daily runs were along the Embarcadero off Fisherman's Wharf up to Ghiradelli Square. Then I started having knee pain and stopped running because it was very uncomfortable and pain would flare up after 15 minutes of running. It turned out that it was my IT band. It was tight and I didn't know how to loosed it up.
Once I started rolling out my IT band with a foam roller. The pain started to subside. Now I can run perfectly without any pain. I make sure to stretch, be well hydrated, and roll out my IT band.
As for the Vibrams, my sister is a triathelete and recommended I try them. I bought a pair and tried it. You really have to start off slow with them. I pulled my right calf muscle and was sidelined for two weeks. But after using them, I feel like I have a better running form and my legs feel strong and balanced. I've only used them for the treadmill, since they do look awkward in public. Plus I'm not sure if I'd like to run without any cushion on asphalt or concrete.