tip off that Miranda was bad was when she said, "What if I told you the the scientist is dead?" Nolan tried to throw us off when she rejects the other millionaire on the grounds that he's selfish but she comes off as kind of cold in the initial scenes anyways.

I think I know how batman survives the blast.
There was the discussion w/Lucious Fox about the auto pilot in the beginning of the movie. Not being broken just fox not being able to figure out how to work it. "A better mind than mine" he said (or something to that effect).
Then when they were scrambling to hook the bomb to the batplane, catwoman suggested that batman get it going out towards the water then eject out. Batman says no autopilot. Fox makes a comment about not being able to figure it out and the look on batmans face was that of being pissed or annoyed at that comment. My guess is that on his way out there, he figures it out, puts it on autopilot and ejects.

You may be right, Budman, but I thought I remembered a bit at the end where Fox is going over some forms with some garage techies, and one of them says something about the autopilot being updated a few months earlier. At which point Fox gets a surprised look on his face. And right after that we get the scene of Alfred at the restaurant in France, raising a glass to Bruce and Selina. But maybe there was some part of the autopilot that Bruce did only figure out at the last minute, as you say.