The Potters did not know that Voldemort was after their son specifically, only that they were in general danger from the Death Eaters by being opposed to them and also active members in the Order of the Phoenix. At this time, they were hidden by the fidelius charm, which is some pretty serious magics: "As long as the Secret Keeper refused to speak, You-Know-Who could search the village where Lily and James were staying for years and never find them, not even if he had his nose pressed against their sitting room window!"

Voldemort only went for their son after Snape told him of Trelawney's prophecy, which was immediately after it was spoken, making very little time for McGonagall to inform Dumbledore and for the OotP to react. (Even supposing they could decipher the prophecy instantly.)

Also, the note from Dumbledore specifically says that James left the cloak in Dumbledore's possession before he died. (Maybe to prevent it from getting into Voldemort's hands.) This explains why the cloak was not available when then Potters needed it the most.

I would care about aliens that I could get along with.

Think about what would happen if Dumbledore (strong wizard, has all sorts of authority) cast Finite Incantatem on his desk, and the spell doesn’t include a “do what I mean, not what I say” security feature.

There must be thousands of spells in that general area. Even if for some reason the desk wouldn’t be disenchanted (which probably it wouldn’t, else casting Finite on someone holding a filled magic pouch or near a magic trunk would be very dangerous, and someone would have mentioned that in MoR), it still probably has dozens if not hundreds of other spells, and can thousands of magic items due to recursive space folding. Even if many of those are protected against Finite, they are so many in total that it’s very likely that a lot aren’t.

Now that I think about it, casting Finite on something you don’t know about sounds just as dangerous as casting a spell you don’t know what it does. (Basically, Finite means casting the reverse of a spell.) Very exploitable unless something automagically checks for corner cases.)

Upon reading these past few chapters I think that Harry has invented a spell to download Hermiones brain state just before her death and this is what we are seeing with the whole soul explosion when she dies.

We have never seen this happen so far at all in HPMOR, and I would think if this is a common thing then when Dumbledore is trying to prove to Harry the existence of souls this is the evidence he would use to try and prove it to him. The fact that he did not and this only seems to have happened during this one particular incident suggests to me there is something going on.

Also it's been completely sidestepped afterwards Harry doesn't ask dumble does anything about it this chapter when speaking about Godric's sword which he would do if he didnt know anything about it. Dumbledore doesn't mention it because he doesn't know as he appeared after and he sent back instruments in time he didnt go himself so they didnt pick it up.

And when Harry is sitting outside the room with Hermione in there is a big paragraph where he ponders why magic works the way it does and why it requires a wand. This feels really out of place and I think is there to show Harry's thought process in making this discovery.

It is notoriously difficult to trail someone who is wearing the True Cloak of Invisibility, with added anti-detection charms because apparently the Deathly Hallow just wasn't enough.

Well, I think Lucius probably made sure a long time ago that everyone knew what Dumbledore (supposedly) said to him. I didn't get the feeling from that scene in the Wizengamot that Dumbledore-killing-Narcissa was any kind of a secret idea that people were just then finding out about.

This does rather change my view of some of the peripheral details, though. Previously, one possibility I pictured was Dumbledore restraining Amelia from her vengeance until Aberforth died, then relenting. I knew Amelia Bones wasn't in the OotP, and I knew she felt distaste at Dumbledore's softness, but somehow I never completely drew the conclusion that she wouldn't care one whit about what Dumbledore said or thought, and therefore probably wouldn't have cared if he had tried to restrain her.

Perhaps more likely, then, is the other way I pictured it: that Amelia couldn't get to Narcissa by herself, and after Aberforth's death, Dumbledore actively approached Amelia and said "Okay, I'm ready to help. I'll be the ward-breaker, you do the deed."

This was my thought as well, but Harry would have had to be unreasonably sure that Dumbledore didn't have some kind of "de-Transfigure everything in sight" spell to use on him.

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Lbhe gurbel vf abg penml, ohg vg'f yrff cebonoyr guna gur Qhzoyrqber gurbel fb sne nf V pna gryy.

A nice touch when Harry is fighting the troll: When he engages his killer instinct, from then on the troll is only referred to as the "enemy", in one case even with a capital E.

Interestingly, while Harry explicitly mentions "censors off" (concerning no more screening off of potential killing methods), that mode of thinking also engages other filters, dehumanizing (de-troll-izing) the creature he's fighting and only seeing it as "the Enemy".