Villain was pretty nitty about 40 hands running 15/2/2.

PokerStars No-Limit Hold'em, $0.05 BB (9 handed) - Poker-Stars Converter Tool from FlopTurnRiver.com

Button ($14.01)
SB ($1.95)
BB ($4.28)
Villain (UTG) ($2.59)
UTG+1 ($5.82)
MP1 ($4.83)
Hero (MP2) ($13.56)
MP3 ($7.81)
CO ($9.97)

Preflop: Hero is MP2 with A, 9
Villain calls $0.05, 2 folds, Hero bets $0.20, 2 folds, Button calls $0.20, 2 folds, Villain calls $0.15

With A9s I dont mind raising from this position. The remaining players had some nits and a bunch of 30+/5/x. The BTN was running 50/2/x so I was happy to have him call...

Flop: ($0.67) J, A, 4 (3 players)
Villain checks, Hero bets $0.55, 1 fold, Villain calls $0.55

I bet my TPMK b/c I am likely ahead of the BTN and dont want to give a free ride to anyone chasing a draw. If Villain has missed he would have folded as well. The call station folds.

Turn: ($1.77) Q (2 players)
Villain checks, Hero ?

Villain checks, I put him on a loose range of good FD's and took hands like AK, AQ, AJ out of his range. I think he bets those on the flop and turn to charge for draws.
If he has an A then it is probably AT and A7-A9. I don't see him calling preflop with worse than that Ace given his stats.

This is where I am torn. I put the chances of a FD higher than him having TP. If I value bet my TPMK, there arent many Ace combos that he calls with on the flop and turn that I beat.
I can bet to protect my TP vs a FD but now I also have the nut FD...
What is my line here that max's my EV?

If I don't hit the flush and the 3rd spade doesn't come, do I check it down? Or bet my TP? If I check turn, he probably thinks that I don't have an Ace like I represented on the flop.
I am at a loss of what the best line is. I really dont get into a lot of hands where I have FD possibilities...