Something tells me there are two timelines for this particular series, the first is from the companions point of view (not quite represented correctly from the actual episode order) of Asylum, DOAS, POT, Mercy, Angels and The Doctor's viewpoint of Angels, Asylum, DOAS, POT, Mercy (Mercy being a standalone portion of the missing 7 weeks because we see Rory losing a phone charger under the bed in one of the scenes) The Doctor is spending more and more time away from them for two reasons, the first is he needs to steel himself for their inevitable loss, the second is the difficulty of acquiring Rory and Amy due to the timey-wimey nature of their demise...