Super interested to hear what other people have to say about this because i would be a touch confused in your shoes.

I think that the combination of the flop check raise + our stack size leaves us in a lot of tricky spots on the turn, any A,K,Q,9,8,7 is uncomfortable. If we donk flop instead, we end up donk/3betting or just being called and in both cases turns are much easier. 

Here we are committed if we bet any more than $4 and committing against AQ/Q9 sucks. I think this is a check (pray he checks behind) fold, K is awful :)

So, you played lets say standardly, though I maybe 3-bet pre even from BB, but call is okay.

C/r OTF is good planned move, but I would maybe bet pot so I could stack off on "blank" turn ( any 2-8 = 27 cards). 

This turn isnt good, but only "good" thing is that we have 99 and we do block his Q9 combos he calls your c/r with, although when he calls c/r - whats his calling range in your opinion then having in mind your holdings?

Also we should be aware that he might have either boat with AKQ type of hand or maybe he turned top set w/ KKQhh type of hand where he has multi-redraws to nuts and he is pot commited meaning you have no FE vs already better hand w/ better redraws (when he has KKQ).

Very important fact is that he bet flop and called your c/r(with bare nut gutter not having AKQ he checks back I think), so AKQ is pretty much in his range when you have JJ99 (reduces KQ9 combos, meaning also increases AKQ combos). He does not have TT neither...

I think we are behind on turn in such scenario, and I would personally do very hard c/f when he value bets as I just dont see any hand but 2 mentioned ones with which he called your c/r OTF... Maybe AAQ (w/ bdfd).

I also think that leading this kind of board would be a lot better unless we can get most of our stack OTF with a c/r. This board obviously hits a lot of ppl ranges and i dont expect ppl to cbet here with air often because they will get called too often and they will check back a lot of hands that have some value so the only hands that will cbet are 2pair,sets,pair and a draw or just a big draw.

Since you decided to c/r flop this can put you in some tricky spots. When he calls your raise i think we can narrow his range to only straight draws. Now the question is just what kind of draws he has. I doubt that he has a lot of Q9 here cuz we are blocking two of them. I think he will very often have AKQ here, which actually would mean that check decide OTT would be best depending how much he bets. It really depends on your opponent if you think that he would call a raise with just OESD. If you do think that he could call the flop with only KQxx or KQTx then i would certainy jam turn!

I think you guys are being way pessimistic if you think people are folding AKJ*, KQJ,KQT, AKT, AAK,QQK, etcetcetc to a single c/r on the flop.