2. Faulty equipment would explain one group of anomalies, ie either the radar image or the infrared but both? Probably not.
3. Probably the best bet. Pics are genuine, just who knows what they show.
3.1 If this was manufactured by an intelligent species, then it actually makes sense that it would be visually cloaked but not necessarily cloaked in other ways. If anyone would already know that something strange is out there, it's those flying already in the sky. A simple observation of our media would show that any reports of ufo's gets laughed at, generally, or not revealed at all. I don't think it's a problem at all. Look at it this way, would it be better to be viewed by masses or by one pilot that will probably be viewed as "off his rocker" for admitting it.
3.2 I'm not aware of any natural phenomena that would behave like this either.
3.3 Possibly but what is more plausible, time distortion or the possibility of life in this massive universe outside of what's on our own planet. I'll take aliens. It's one huge universe out there. :)
I think what leads to them being intelligient is the fact that they fled when pursued and surrounded their pursuer at one point. Interesting that they didn't attack.