assuming that Dumbledore should be able to make a good estimate of Quirrell's speed and the time he spent traveling. I also think that Dumbledore should have noticed when Quirrell stopped, since by then he had already returned to Hogwarts.

How would he? He was not with Quirrel nor was he presumably examining the Map (if he had it).

Fred and George spent quite a long time fighting the troll

Not really? They spent maybe 30 seconds at the outside - it doesn't take long to cast a bunch of spells and swing a sword once. In the real world, fights do not last very long. Only in movies do fights go on for entire minutes.

however, if Dumbledore were to actually ask Harry about this, Harry would of course tell him that, no, Quirrell isn't able to cast any magic on him, which would probably be enough of a hint to lead Dumbledore to the correct answer.

Dumbledore would have to ask, though, and why would he when he would expect Harry to be ignorant? I would also note Quirrel's own explanation to Harry about a 'cursed artifact', which is a likely and also fully general explanation which Dumbledore could not compel a peer of his to explain his secrets, not in a culture like Magical Britain.

It's hypothesized both in canon and in Methods that Harry and Voldemort might have a connection of some sort.

Based largely on the events at the end of Stone, which never happened in MoR; in MoR, the only basis for this speculation is Harry being a Parseltongue. A passed on ability doesn't suggest a live physic link.

it seems like it's something that Dumbledore and McGonagall might rate as high-probability conditional on Quirrelmort theory.

Do they? Everyone seems quite satisfied with the David Monroe theory.

(And I can't imagine that psychic bonds are unheard of in Methods-world.)

We have no idea.