1. Wasn't The Question Asked At Trenzalore...Twice?
Yes, it was. From the Doctor's perspective, the first time he visited Trenzalore he believed he was there to answer the question; this was in 'The Name of the Doctor', remember? He saw that he died on Trenzalore, and that must have been when the Daleks attacked at the end of 'The Time of the Doctor'. He changed that future, and survived that attack. Well, Clara changed it by speaking to the Time Lords. The Great Intelligence and the Whispermen wanted the Doctor to answer the question, "Doctor who?" so that he would open his own tomb, and allow them access into his timestream. Given that the GI was purely information, he'd have known the question was referring to the Doctor's final battle on Trenzalore, and probably used it to scare the Doctor into opening his tomb. The Silence couldn't have known that the Great Intelligence would also ask "Doctor who?", but they are a religion; it's not that far-fetched to assume it was prophesied.
