Why would you 3bet this hand preflop ? Dont see a good reason why

You bet the flop with J high and a backdoor flush draw because you know you are completely behind his 3bet calling range, then you check on one of the few cards that improve your hand and probably put you ahead of villain's holdings {in order of personal preference: 8s, Qs, J, T, any spade, Q, 8, K, 7}. Now you fold the river giving him exactly a set after you showed weakness and your hand remains top pair?

Or should i be betting the turn to get AK to fold so he doesnt bluff on river?

you don't prevent villain from bluffing when you hold solid bluff-catchers, you prefer them to bet because you making more in the hand

but where did this all begin... your reasons for 3betting this hand remain unclear

JTs is a fine hand to play in position, so long as the blinds aren't squeeze happy. 

When you 3bet this hand and villain calls (and i presume he had a tighter opening range since you immediately have him flatting AK/TT to a 3bet), you are [clearly] lost postflop. make things easier by playing a smaller pot in position. 

if villain is such an incredible nit that his river bet beats high pair here 100% of the time then flatting JTs and raising flops/turns/rivers would put him in more pressure. As a nit he avoids those situations at all costs, so play toward his weaknesses not his strengths

SB/BB appear to be weaker players due to their stack sizes. JTs plays very well mutli-way and in position. So unless you have a very strong reason for 3-betting here pre-flop, I'm not a big fan.

Before you 3-bet or call, think about how you are going to win money from the pot. At lower stakes, maximizing your exposure against weaker players and value betting them hard is how you win money. Suited connectors are mostly only good semi-bluffing hands against regulars who create aggressive dead money. If you 3-bet a hand like JTs against someone with a strong calling range, you are essentially isolating yourself as the fish.

Your range analysis may be a bit flawed. When you say 99+ are you including QQ-AA? QQ-AA will possibly 4-bet pre-flop and so would AK. So those hands are likely not in his 3-bet calling range. This is where reads and/or stats are really important, which you forgot to include.

As played, he could certainly have sets and overpairs in his range, as you mentioned. But like Daz said you have played this hand using a very weak line, which may have induced bluffs from hands like AQ, AJ, and KQ. Each of those hands have 16 combos, for a total of 44 possible bluffing combos (AJ only has 12 combos because we block a J).

There are 13 combos of 66, 99, TT, and JJ.

Final pot is $7.55 and it's $3 to you, so you need to win ~ 40% to break even here.

Even if villain is bluffing with only a third the combos I mentioned above then it's a call.