5) Riddle can't use Parseltongue to prove stuff, that only works between wizards of roughly equal power. If you're much weaker than Riddle, you never know if you've been False-Memory-Charmed to hear Riddle say something in Parseltongue. (Even Harry can be charmed this way, Riddle just needs to ask a minion to do that.) In any case, there's no need for Parseltongue. We know that Voldemort has threatened Death Eaters in the past, and presumably kept his word. Snape is a former Death Eater, so he would believe Riddle now.

6) The obvious way to single out Lucius is to provide proof that he wasn't Imperiused to become a Death Eater. Since Riddle is the one who didn't Imperius him in the first place, such proof shouldn't be too hard to find.

On the other hand, if you choose to frame Lucius for burning Narcissa, the obvious motive is infidelity, or betraying Death Eaters to Dumbledore (as she did in canon at some point), or any number of other reasons why people kill their spouses. And if you imagine yourself as Lucius, then accusing Dumbledore afterwards is also an obvious move, because you don't want to admit to Draco that you've killed his mother, you know that Dumbledore had a clear motive (see the bit about Aberforth in Ch. 82), and no one else would be crazy enough to attack your family.

HPMOR has just too many plot devices! I can probably justify anything at this point. Maybe I should write an alternate explanation of everything that happened before the Truth arc, because Eliezer's explanation doesn't feel very satisfying to me, to be honest.

If Dumbledore had kept the Map himself - if the Weasleys had ever spoken of it to Dumbledore - but they did not, thankfully.

Calling out explicitly why this is confusing:

The trapdoor had hardly slammed shut above them before all nearby sounds muted and the old wizard spun on them and held out a hand and commanded, "Give me the map!"

"M-map?" said Fred or George in total shock. They'd never even suspected that Dumbledore suspected. "Why, w-we don't know what you're -"

"Hermione Granger is in trouble," said the old wizard.

"The Map is in our dorm," George or Fred said immediately. "Just give us a few minutes to get it and we'll -"

The wizard's arms swept them up as if they were hugging-pillows, there was a piercing cry and a flash of fire and then the three of them were in the third-year Gryffindor's boys' dorm.

The Weasleys quite definitely told the location of the map to a Phoenix wielding, sorting hat summoning, line of Merlin holding person who looks like Dumbledore. So either Quirrell is lying, or someone Obliviated the Weasleys before Quirrell stole the map from them. Further, Harry knows this.

If the enemy can notice you running off to consult the Weasley twins during class after Hermione was arrested, and find out about that magic map you said was stolen, then the enemy can wonder why I was guarding Hermione Granger's body.

By the way, that line was edited. It originally read:

If the enemy can notice you running off to consult the Weasley twins during class after Hermione was arrested, and find out about their magic map and steal it, then they can wonder why I was guarding Hermione Granger's body.

From discussion context, I believe the line was edited because it wasn't clear how Harry could have learned about the map on his own and people were theorizing that Harry stole it himself.

I am assuming the goblet is borrowing the natural language parsing of the people subject to it, sorting hat style. And no one not being argumentative on the internet would read it that way. Which means it really is a flawless blanket protection from intentional harm, and the blood part is utterly redundant.

As for why I'm so sure Voldemort is wrong:

Well, there is the outside view, in which I just have trouble with the idea that a 16 year old virgin is a sufficiently supreme plotter, manipulator and cold-blooded killer to pull this off on someone who has been a feared witch for centuries. Not impossible, but very low probability.

A witch who can look like whatever she feels like and who is a byword for "Scary badass" inspiring crushes and devotion in her pupils? Pupils that are utterly safe from her? Odds: Nigh-Unity.

Also, it just doesn't hang together logically. Baba breaks the contract and then Perenelle kills her? Double-dipping on the causes of death, there.

I could see it being an accident, in which case that counts as one of the most traumatic consensual sexual debut's I can recall reading about, ever. That is where I put most of the residual probability. 30 some percent.

But as an intentional plot ? It has way to high a chance of going wrong. Anyone able to think it up would know better than to try it.

Well, Harry hasn't actually tested the idea that wizards can suffer brain damage the same way as Muggles. He just assumed they do. But it's a reasonable assumption.

What happens if you progressively damage Quirrel's brain? At some point Voldemort will either decide or be forced to go and possess another body or Horcrux. That thing-which-goes-off is for all intents and purposes a soul.

A backup isn't a good description, because Voldemort is always aware - there's no point at which he exists only as a backup and may or may not be restored. Also, a backup implies restoring multiple instances, and creating multiple backups; the True Horcrux doesn't seem to do that.

Snape's head snapped around, as Professor Sprout raised her wand, and the Potions Master managed to raise a wordless translucent ward between them. But the bolt that shot from Professor Sprout's wand was a dark brown that produced a surge of awful apprehension in Harry's mind; and the brown bolt made Severus's shield wink out before they touched, clipping the Potions Master's right arm even as he dodged. Professor Snape gave a muffled shriek and his hand spasmed, dropping his wand.

The next bolt that came from Sprout's wand was a bright red the color of a Stunning Hex, seeming to grow brighter and move faster even as it left her wand, accompanied by another surge of anxiety; and that blew the Potions Master into the door, dropping him motionless to the ground.

I interpret that as Legilimensed Sprout's magic is Voldemort's magic is Sense of Doom magic. But then how was the troll made immune to sunlight, when Harry touched the troll's skin directly?

I still think the illness is faked to give everyone a ready suspicion as to the nature of his inevitable failure as defense professor at the end of the year, rather than the true reason.

That could just be a feature of the True Patronus, which is pretty anti-death and especially anti-indifference-to-other-people's-lives.

Harry made some serious mistakes in chapter 105.

First, the parseltongue honesty-binding could just be Quirrell's (selective!) wandless magic--I mean, he just forged a note "from yourself" (and why do you even MAKE a self-recognition ("I am a potato") policy if you just forget all about it once you're in a life-stakes intrigue) so you need a lot of extra suspicions going forward. But assuming it's real... there are crucial questions Harry can now profitably ask, with his help conditional on getting immediate Parseltongue answers, along the lines of:

"Why did you set up this elaborate ruse instead of just asking me? Most of what you're saying right now sounds like something I would've probably agreed to if you were open about it, but no, you had to pretend you were dying and kill my friend, so it sure seems like you're planning nefarious things I'd rather not aid even at the cost of my life and the hostages' lives... does my CURRENT utility function actually prefer your planned results to the death of me and the hostages?"

(This isn't the perfect phrasing; for one thing Quirrell doesn't necessarily know Harry's utility function to high accuracy, for another Harry might have disagreed to the "open" proposal at weaker dispreference than "this is worse than my death". But something similar...)

Iff Quirrell is at all "innocent" at this point, he'd want to answer these, and never mind the "my policy is never to reveal that much or people will know I'm guilty later when I actually need to keep mum" stuff; these stakes seem high enough to outweigh any future similar dealings. If he's guilty, then just die like you'd apparently prefer.

[the only edits I made here after getting responses were to correct my spelling of "Quirrell", and this note]

Your point 2 is another thing I'm getting pretty suspicious of. Quirrell has set up a very long plan, and could easily have faked this effect with wandless magic, or an enchantment he could later dispel, all along.

Were any of these said by Quirrell as a snake, as opposed to Parselspeaking as a human?