Re: Kate Stewart in Day of the Doctor (SPOILERS!)
It's looking like we'll have two options as to how reconcile things:
1) Ignore the original dating of Amy and Rory's present day adventures with the Doctor.
2) Ignore the 2013 date for Day of the Doctor, and assume it takes place several years in the future.
Probably the first one. For all we know, he did meet Amy and Rory earlier than before in the rebooted timeline, with the Daleks invasions having never happened as a result of the crack in time.
The latter date will probably be the one thats adapted, though.
"Spock...?" Kirk said, whispering.
"I am... most pleased to see again, Captain" Spock formally replied.
McCoy shook his head in disgust. "Oh, for crying out loud, Spock. Its been eighty years!"
"Seventy eight point four years, Doctor."
The Holy Three meet again, in The Return