This is my first post to this forum so hello everyone.
To respond to the OP I am in the same boat as you but convinced that the sizing chart on Vibram's website needs some work.
I'll start with saying that if I was buying a pair of NewBalance sneakers I'd go size 7 4E so basically I stand on squares. I measured my foot per the instructions and came to about the same thing you did, W39 (9 1/4").
My first pair of VFF was the TrekSport that are M40. They fit great in the toes and midsole but have like 3/4" on the heel which isn't a terrible thing since the way the straps work. I wore them for a week exclusively and they were ok. I decided I wanted a pair of KSOs and Classics so I headed back to my hip shoe store.
I walked out with a pair of the agate classics and KSOs in the clay/green colors. First there was a noticeable difference in colors (the blacks just didn't fit) which others have noticed. I tried them on in the store and both felt great but after I got them home and walked the dog in them the classics I think are too small (I just did the cord cut mod to see if that helps) esp in the toe pockets. The KSOs are just about perfect.