Im confused. Help please. 2-5 nl. All streets confused.

[ExLAx]

2-5 nl game at b&m club. 9 handed.

Lag but solid postflop player to immediate right raises to 20 in EP+1. Hero has black Jacks, calls 20. Button Calls. 3 to a flop.

Q56 two diamonds. Queen is not a diamond. Lag bets 35. I call. Button folds.

Turn: 8 diamonds. Lag checks, I Check.

RIver : A diamonds. Lag checks, I bet 60. Villain calls with 89 9 of diamonds.

A few questions. On that flop, should be inclined to call because I could take it away later + i might have the best hand+ a call will probably gain me the same benefit/info as a raise here? I realize I checked the turn with the best hand and with a board with my oppenant probably drawing to at least 9 outs. Was My river play was bad since he either paired his ace or will call with a medium flush after I checked the turn?

So, should I bet turn here with a 3 flush on board since Im either drawing dead and have him drawing to a bunch of outs? How is this different from a pot control turn check situation? am i not trying to control the pot because my opp has 1. a lot of outs 2. I likely have the best hand 3. I am not trying to induce a bluff on this board?

MY river bet is bad because there are a lot of hands that will call that beat me and I am not likely to push many hands I beat off?

My logic is lost, please help.