Well, now that we know on when the events of this film take place, that still leaves the mystery of why SHIELD was absent from Iron Man 3.
We know that based on the events of "Agents of SHIELD" that the Extremis virus is on their watch and you'd think that they'd show up all over the scene if Tony was attacked by the Mandarin and presumed dead for awhile.
I think AoS is after IM3