I noticed something odd in chapter 17, which seems relevant:

Harry was rather confused. "But this could be important, yesterday I got this sudden sense of doom when -"

"Mr. Potter! I have a sense of doom as well! And my sense of doom is suggesting that you must not finish that sentence!" ... "This isn't like you!" Harry burst out. "I'm sorry but that just seems unbelievably irresponsible! From what I've heard there's some kind of jinx on the Defense position, and if you already know something's going to go wrong, I'd think you'd all be on your toes -" ... "I see," Harry said slowly, taking it all in. "So in other words, whatever's wrong with Professor Quirrell, you desperately don't want to know about it until the end of the school year. And since it's currently September, he could assassinate the Prime Minister on live television and get away with it so far as you're concerned."

Professor McGonagall gazed at him unblinkingly. "I am certain that I could never be heard endorsing such a statement, Mr. Potter. At Hogwarts we strive to be proactive with respect to anything that threatens the educational attainment of our students." ... "Oh, I doubt that, Mr. Potter. I doubt that very much." Professor McGonagall leaned forward, her face tightening again. "Since you and I have already discussed matters far more sensitive than these, I shall speak frankly. You, and you alone, have reported this mysterious sense of doom. You, and you alone, are a chaos magnet the likes of which I have never seen. After our little shopping trip to Diagon Alley, and then the Sorting Hat, and then today's little episode, I can well foresee that I am fated to sit in the Headmaster's office and hear some hilarious tale about Professor Quirrell in which you and you alone play a starring role, after which there will be no choice but to fire him. I am already resigned to it, Mr. Potter. And if this sad event takes place any earlier than the Ides of May, I will string you up by the gates of Hogwarts with your own intestines and pour fire beetles into your nose. Now do you understand me completely?"

As Harry observes, this exchange is extremely out of character for McGonagall. Telling Harry not to voice his concerns about Quirrel, I could believe; but cutting him off mid-sentence, and them making such a graphic, violent threat if he does, I can not. It is so out of character, in fact, that I think it must be a symptom of being Imperiused.

We know that Voldemort used to use Imperius quite a bit, and the only real reasons he might stop would be if someone figured out how to detect it (which hasn't happened), or if his new form didn't have the power. One Imperiused person rules out the second possibility, so if if Quirrelmort put an imperius on McGonagall, he has almost certainly used it elsewhere too.

Which brings us to Harry's attempted breakout of Bellatrix. Breaking in to Azkaban to rescue Bellatrix Black, I could just barely believe. Pretending to be Voldemort while doing so, however, pushes credibility too far. From Chapter 52 to Chapter 54, Harry is Imperiused. There are just too many things stupid and suspicious about the plan to believe that Harry overlooked all of them.

And that brings us to the question of what Imperius actually does. And this, I think, explains the chapter title, "The Stanford Prison Experiment", which otherwise seems not to fit at all. The conclusion of that famous experiment was that if you give someone a role - even a fake role, like a prison guard over subjects in a psychology experiment who are technically free to leave - then they adopt it as part of their identity, including the evil parts, and become blind to the wrong things they do as part of that identity. So perhaps that's what Imperius does: it assigns its target a particular role, which their mind will bend to accommodate. That would also explain why the title was redacted for part 1, which takes place before the Imperius curse was cast.

Here are some abnormalities in Harry's mind:

This was it, this was the day and the moment when Harry started acting the part.

And in another part of him, like he was just letting another part of his mind carry out a habit without paying much attention to it...

Professor Quirrell had instructed Harry, calmly and precisely, how he was to act in Bellatrix's presence; how to form the pretense he would maintain in his mind.

The only problem with this theory, is that Harry believes that Quirrel can never use magic on him. His Patronus and Quirrel's Aveda Kevadera certainly didn't interact well, and there seems to be an issue if they touch. But the theory that they can never use magic on each other, seems to have appeared from nowhere; there is no evidence for it whatsoever, except the sense of doom. Perhaps that idea was planted, to make the idea that Harry was Imperiused seem less plausible?