Doctor Who

1. When was Amy replaced- Somewhere between last years xmas special and the opening of series 6. Just before they go to America. Or so the Doctor seems to think- another possibility is when she is captured by the Silence and they tell her she has been there for days and she is nearly ready.
2. How did the Doctor figure it out- the first clue was the Tardis being unable to determine if she was pregnant or not. The Flesh two parter- Rebel Flesh- the Doctor already knows about the Flesh and he is just going to investigate its origins- so he knew by then. Although he doesn't seem to know for sure until the end of that two parter. He couldn't say anything because of the Silence, there could be one standing right next to him and he wouldn't remember it was there.
3. The Silence are a religous order- what they call the Silence, the 'forget them if you look away aliens' may be Silence or just servants of the Silence- that is yet unresolved (I favour the latter as I still think Omega is behind the whole thing).
4. The Doctors Death- it was never the Doctors Death which was a fixed point in time- everyone just thought it was because thats how it looks. He was always in the tesselector, in the first ep of series 6 when he is shot- thats the tesselector. It always was. The Tesselector being shot with the Doctor inside it is the fixed point. So Time is not tricked, everyone witnessing the event is. And the Doctor being the cold, ruthless bugger at need that he is, that tricking extends even to Amy and Rory. That is why before the second shot he turns to look at Amy and says "I'm sorry", not for dying but for having to trick her into believing he is dead and for the pain that's going to cause her. (And it has to be convincing as the Silence are there watching as witnesses- Amy sees one of them on the beach in the opening episode of series 6)
5. Mels- regeneration is different for every Time Lord, its not precise and some have more control over it than others. The Timelord Romana chose her own look and tried out several different ones before the pattern 'set'. When Mels turns into River she says she might take her age down slowly just to freak people out, so she seems to have more control over her change than the Doctor does, he can't even make himself ginger like he wants! Mels was a, roughly, 6-8 year old girl in the orphanage and that was New York in 1968. So she is actually at least 40 in human terms by the time she is growing up with Amy and Rory. Also when she regenrates into River she says the last time it happens she became a toddler- so she regenerated into a younger version -which must have been mighty confusing for her!-so its hard to tell how old she should look or to know how much control she has over her aging-some at least from her comment about taking a few years off to freak people out. In general Gallifreans and humans age in appearance about the same speed until puberty is passed then Gallifreyeans age a lot slower. There is also the Silence's time machines to take into account. It is even possible Mels used one of them to get to Amy and Rory's time- possibly even the one from the Lodger episode in series 5. And a final option is that, given her role was to kill the Doctor and the Silence knew eventually he would turn up for Amy that she was deliberetly planted there by the Silence to await the Doctors arrival. After she regenreated in New York she was recaptured and moved to Amy's time- this is my own favoured option. Moffat however leaves it open enough and with enough clues that the viewer can puzzle out how they think it was done for themselves- its one of the things about his writing of Who I like.