I think you're being too hard on yourself. You had a flush on a paired board, with a possible straight flush out there. Your hand was the 5th nuts (not giving him KK/QQ or 93).

V is in the BB, getting great odds to call with almost ATC pre.

You checking the flop multi-way sandwiched between the blinds and the BTN seems fine, and maybe optimal.

His x/r on the turn is a strong play, but if he's good, he could have a straight, a flush, a boat, a straight flush, trip 9's, or possibly some bluffs. We're ahead of his pre-flop calling range, but our hand isn't invulnerable against his turn check-raising range. We wouldn't expect him to turn many made hands into check-raise bluffs.

I think an argument could be made for 3B'ing turn or raising river, but a counter-argument could be made for taking the more defensive path to protect our stack from a cagey opponent capable of turning a strong hand into a bluff.

If we did 3B turn, he's folding out almost every hand we beat, making his range that much stronger. He could 4B, or flat call with a plan to bomb the river.

Once we flat his turn raise, and he takes this small sizing on the river, I would be tempted to put in a smallish raise, because his sizing looks fishy following the turn x/r, but there again, he could be taking this sizing to induce a raise, planning to 3B, either for value or as a bluff.