$65 MTT @ Muckleshoot in Seattle. 112 entrants.

We are on the first level. 50-100 with starting stacks of 10K. I have slightly below average stack ATM. I live across the water, so I'm not a regular here and don't have any solid history with any of the players.

One person limps in front of me and I make it 550 to go with AK. Everyone folds around to the limper who somewhat surprisingly calls my raise. I was expecting a fold.

Flop is A97 with two clubs. He checks to me and I bet 800 into a pot of 1250. He calls. Turn card is an 8. He checks to me again and I consider checking for pot control and to keep it small, but there are so many river cards that can fall where I'll have no idea where I stand... so I decide to bet 1600 into a pot of 2850. My opponent tosses out 2500. 2 1000 chips and 1 500 chip... so clearly: not a call. The dealer makes him min-raise it to 3200. I'm sort of perplexed. Dude doesn't look like a noob and I assume he knows what he's doing. I don't think he's accidentally raising me here... However... there's enough doubt in my mind that I decide to call the raise and see what he does on the river. A on the river and he ships for around 5500 and has me slightly covered. I have about 40% of my chips in the pot and just rivered trips with the nut kicker.

What do I do?

So, 14750 in the pot and you have ~5000 left right??
are the turn/river card is club??
Imo, either fold turn if you have soul read that he had you beat or definitely call river! you can't fold now. If he is decent, with set he would c/r you there rather c/c otf when fd is there, still he could take the line for deception though. The turn minraise is kind of representing set/2p/straight but can have AQ,AJ as well.
otr, if no fd completes, we can beat AQ,AJ and chop with AK if he played it like that. Having an A in his hand very unlikely though. We are beaten by 66,77,88,T9. As per your read, I discount A8,A7,A6 as he might not call those pre with such a raise sizing. 66,77 otf is possible for deception. 88 should not follow after the flop. So, 66,77,T9 are his possible holdings. though calling with T9 pre is bit tough imo but not impossible when you are so deep. calling the flop with Tc9c is actually very possible.
Pre, I'll raise less (3.5x)
otf, fine imo
ott,I would fold over his min raise as we are so deep and I don't feel to commit in the pot with TPTK.
otr, you have priced yourself in imo.

Open smaller, 350-375. Ck behind on turn, not gettin 3 streets from anything. As played fold river, you never have the best hand, sorry you ran into a boat.

Open sizing is fine this deep and in a live game imo.
b/f turn is ok

I have a limper in front of me and I don't want to encourage a bunch of people to call behind me by making a smaller raise. I'm UTG+2 I think and I'd rather just take it down preflop or get heads up with the limper. So I like my raise size.

I was planning to bet-fold the turn but the way he put his raise in the pot made me want to see what he'd do on the river. I wasn't entirely convinced he even meant to raise. However, when he ships river even though another A hits, I think I'm beat here the vast majority of the time. I folded.

I asked him if he could beat AK and he initially said no... but then later he told me he had 99... which makes a lot of sense. I ended up making a deep run in the tournament... and actually stacked him later.