I would say that, as you intend to shoot this yourself, you can pretty much write this in any way you choose. If you want your actors to ad-lib their dialogue, you could make do with a rough shot list, or a list of cues you want them to hit and a rough outline of any dialogue, and just roll with that. That would be similar to what they did for "Blair Witch...".
It does beg some questions though, maybe someone could fill me in too, just out of curiousity... If you would write a found-footage script in the same way as a regular narrative script, would the script ever need to mention the fact that it's supposed to be found-footage? Or would a found-footage film start life written as a regular script, no mention of it being found footage, before the producer decides to shoot it found-footage style? What about any mention of the camera-operator? Would they need to be written as JOE BLOGGS (O.C.) at all times, or what?