As the A380 is very quiet, it does not matter where you sit. I like it further back and near the doors. Cos SQ does tend to keep the cabin rather warm and the further forward you are, the hotter it gets!
Back where the loos are, are fine. You really can't hear much especially if you're watching a movie on the noise cancelling headphones or when sleeping.
I don't understand what you mean by 'windows misaligned'. You will get a window / or two with each seat. The only row without a window is row 11A/K. Row 18 D/F are the bassinet seats. Yes you can sleep straight.. but the TV screen is also at a higher level instead of at eye level.