As much as I like theories, I can't say that I buy all of this. The number of windows on a building can't have much importance. If the story did pan out where the moons eye plan resulted in the scenario you presented, or someone interrupted the moons eye plan with izanagi/nami (can't remember which is which), using the number of windows in a building as an anchor to prove this was a well thought out conclusion is very weak.

As you might have guessed I'm a light reader of the manga, and other than the non-sharigan eye of Kakashi I haven't noticed many mistakes. Is there a complete (concise) list somewheres?

I'm sure a manga as popular as Naruto pays well enough for Kishimoto to have assistants. It's possible that these mistakes could have been caused be delegating work so that he has more time to plan out the details of complex storyline elements or get a head start on more complicated battle sequences early.