I also had to re-order a half size down in the 4.0s. My size 11.5 4.0s are actually a little longer than my size 12 original Free Flyknits. I found that they fit narrower than my other Flyknits as well.
No, they weren't limited because they weren't limited. They were available on Nike.com for months and at Nike stores.
They were a wide general release and not a quick strike release of any sort. Great shoe, though.