@End of the story:
The Thing is, that we also thought this of the whole Shinran Lovestory. And then it came much faster than we thought.
Sure, Ran is no Detective, but she isn't an idiot either.(Plus, all the other smartass detectives in the Manga actually found out Conan's secret very quickly. Amuro is an exception, but Shinichi hasn't been on his radar so far, at least for now..) And she already had the theory that their might be a reason for him not telling her during the Cellphone case.
I'm not agreeing with all points on the List made by the OP, since lots of stuff can be explained otherwise.
But there is a point with Ran's behavior having changed a bit. And here reaction to Conan's supsicion debunk at the end of the Eri abduction case felt really like "Ha Ha. Sorry, Deduction Freak, but you used that trick too often. But I'm playing along for the moment..." Or something similar.