Final table $16.50 mtt
Villain (68.38 BB)
Hero (29.04 BB) [9h,8s]
Hero calls from the sb and villain checks from bb
Flop [7d,8d,9c]
Villain bets 1.13 BB and hero raises to 2.61BB, and villain 3bets to 4.09 BB and hero calls.
Turn (10.44BB in pot) Ac
Villain checks, hero bets 6.89 BB and villain calls
River (24.22BB in pot) 10h
Villain shoves and hero calls for 16.93BB remaining and villain tables 10c, 8h for better two pair. Should I be folding or is calling and getting stacked there appropriate?

Your flop raise is really small, villain is getting a price of 1.48bb into ~6bb so you've laid them 4:1 and they can continue with pretty much anything.

Villains flop 3-bet is a literal clickback which is tough to gauge the range for, they should never be doing this in theory so you need to have some reads to decide how to proceed. 4bet shove seems too big (although if you had sized your raise properly it might have been a good 4bet shove spr). 4bet non-allin to call shoves seems fine (read dependent). Calling is good and keeps villain wide if they're spewy and prevents you putting in all your chips when you do happen to have low equity. Tough situation.

Villains check on the turn is strange again. They should rarely give up the betting lead with straights so your hand is now crushing their range. Geometric bet sizing looks good (such that the turn bet will be proportionately equal to a river shove).

Villain leads all in river, taking back the betting lead. What a strange hand. Looks like a fold to me: any 6x or jx gets there (there are lots of these possible, 67, 68, 69, j7, j8, j9, 6xdd/cc, jxdd/cc), T9 and T8 sort of get there and might go for thin value, and there isn't much that's bricked. You can probably call with straights only and be doing fine.

Final table and no mention of stack sizes of the table and prize structure.

Check your ICM and what are you thinking calling on this river.

Depending on ICM I don't even mind flat calling flop.
Slow down on turn after the V called the 3 bet and definitely fold river.

It's heads up mtgalex. ICM factor goes to zero heads up.

If I was unclear it was the final 2 players and the opponent was a weak reg. I felt the 3b on flop check turn represented a lot of 10x, but I also didn’t think he would lead jam rivers with straights, but I guess maybe he is either taking a bluff line with two pair or he soul read me

Sorry didn't get that from the title.
Then flop and turn is fine and river is totally dependent on read whether Villain are capable of shoving enough nonsense.

GTO indicate 9h8s are calling and folding mixed so the hand can go either way depends on reads.

GTO Villains are expected to shove straights and T9o (can't have T8o in GTO here) with bluff like Q9, Q8, 9x and Tx. Not sure your Villain are capable of doing this or randomly bluff using some other cards.