I'm skeptical that physical pain scales beyond 2 or so orders of magnitude in a given span of time. I'm also skeptical of the coherence of death as an ontological possibility.
Being forced to choose between two things I believe are incoherent, I'd pick the torture. I'm more worried that there's a coherent notion of death being referenced than that some entity will experience a level of pain that seems impossible. There's multiple problems with the concept of pain here: it's not clear the entity experiencing it would be conscious during that time frame (especially if they have no memory, as memory is tied to consciousness), it's not clear that entity would be indentifiable as me, it's not clear that upping some pain number actually corresponds to that level of utility, as utility is plausibly bounded over short intervals, etc.
Inquire about the subjective vs objective duration of that millisecond. If there aren't any bad surprises there, pick torture before my mind can try to make a guess of how bad it will hurt.
In the torture vs dust specks I choose dust specks if they weren't allowed to cause ripple effect and if they were guaranteed to be spread with only 1 dust speck for humans. Here there is a similar consideration, how the pain is spread in a time interval so small that it will basically be inconsequential (since he guaranteed that I won't suffer lasting consequences, I'd fully expect such a pain to fry my brain and have it possibly melt out of my eyes or something).
I'm basically choosing to screw over the future myself of that millisecond to protect all the other future self.
Both decisions should work fine as long as I'm not approached by a large number of Pascal's muggers, if it risks becoming a trend I should review my decision theory.
For another human... I'd choose torture for the same considerations, if he choose torture I wouldn't override it, I'd have emotional qualms about overriding his "death" decision, but I likely will.
The math of pain vs pleasure of being alive would likely say my decisions are wrong, but I think the math starts to stop helping in this limit cases, picking death strikes me as a two boxing with Omega (though I think the math there shows you are right went one boxing if you manage to take in the backward causal link). You'll be pretty glad you choose torture exactly one millisecond after and for the rest of your live, and so will the stranger (unless he was suicidal, but it doesn't seem I'm allowed to know it before picking).
Turns out Pascal's mugger is real, and as would be expected of someone who does Pascal's muggings, he's a jerk and likes forcing people to make impossible decisions. Also, his threats are discovered to be truthful and credible. He decides he's sick of mugging after collecting a few trillion dollars from it and wants to try something new. He takes out a gun (killing people with Matrix powers is for cowards) and forces you to make a choice.
Scenario 1: He puts the gun to your head. "I will kill you unless you let me put you through torture 3^^^3 [1] times more intense than anything you can possibly imagine. Don't worry though, it'll only last for a millisecond, and you won't remember it or suffer any trauma or anything."
Scenario 2: He puts the gun to a random stranger's head and tells you to make the choice for them. He freezes the stranger in place with his Matrix powers (2a: the stranger overhears before being frozen and decides on what they would choose, 2b: the stranger is frozen before they know what's happening) so the stranger has no way of communicating their preference to you. He will shoot if you don't make a choice.
Scenario 3: He puts the gun to a random stranger's head and tells them to make the choice. After you hear the stranger's choice (3a: they choose death, 3b: they choose torture), the mugger gives you the option to override it. He will abide by the stranger's choice if you don't make a choice.
What should you do?
In the words of the Torture vs Dust Specks question this was inspired by: I think the answer is obvious [in all scenarios]. How about you?
Footnote:
[1]: The notation is called Knuth's up-arrow notation. 3^3 is 3 times 3 times 3. 3^^3 is 3^(3^3). 3^^^3 is 3^^(3^^3). 3^^^3 is used as an arbitrarily large quantity so that there's no situation where it's "too small".