Just like to make a quick comment regarding one of the possible factors, namely the cargo shift theory.
In my opinion on a plane that is this full, it will be quite difficult for the cargo to shift with only acceleration. Especially one full of pax and fuel for a 10+ hour trip. Now one might say that on these planes, the containers are placed on rollers and can move quite freely. May well be as I don't fly them, only MD-80's. But even IF that was the case, they move to the rear of the plane allowing for early rotation and or difficulty controlling the aircraft. Kind of like the poor chaps taking off of runway 27R back in the day in Miami.
And if so they would have rotated much earlier and become airborne earlier. It does not account for why the plane refused to become airborne after 13,000 feet on a 12,000 foot long runway.
Really interested in the initial results form ATSB.