Plot Holes

I think there's an ever-so-slight difference between the idea of her parents being remembered back into existence and never having been erased in the first place. Had they never been erased in the first place, then you would be right: Amy would likely be living in Scotland still , never having met Rory or even the Doctor. But they weren't unerased, they were written again; a subtle distinction which I believe could explain away the perceived plothole. If Amy remembered them back into existence, then perhaps she remembered them into the situation and scenario she was most familiar with; or maybe her love for Rory was more powerful than that for the parents she couldn't at all remember, and their existence bent to fit hers with Rory.

As for the third floor in Amy's house, I thought the same thing. I thought the house was going to turn out to be a ship similar to the one seen in the Lodger - which the Doctor specifically referred to as someone's attempt to build a TARDIS. Maybe the same ship at a different point in its timestream, possibly owned by whoever's behind "the Silence". This may or may not lend credence to the idea of the villain in question being Omega, the Valeyard, the Master, or some other Time Lord baddy, but that's another discussion entirely.

I think most perceived plotholes introduced by Big Bang Two can be explained away quite easily: when the Universe was rebooted, history shifted in small ways due to the randomness of existence. Some may think of this as lazy writing, but I feel it was the only way for Moffat to have any kind of control over some of his predecessors more... questionable stories. Even being as fond of Mr. Davies as I am, I can't deny that a number of his plots are in desperate need of some wibbly-wobbly adjusting; I don't think many others can deny it either.