WPT Borgata Hand- how could I have played this better?

[Muellagio]

Nearing the end of the first 45 min level, blinds 25-50, stacks are still pretty even, started with 6k in chips. I'm on the button with 99, three people have limped and I raise 4xBB. Only the BB and one other guy call. The flop is J 5 9. The BB bets 400, other guy and I both call (my first mistake). The turn is a 2, BB bets 400, other guys calls and I raise to 2k. BB folds, other guy smooth calls. The river is a king. He checks. I bet 2k, he raises all in for not much more, I call and his straight knocks me out.

I know I made two big mistakes here, not raising after the flop and betting the river, but was my raise on the turn big enough? A raise on the flop would have had the same result probably-should I have pushed here? I didn't because I was worried about him having a set of jacks when he smooth called the raise on the turn, but I put him on AJ or maybe a straight draw. I didn't think he'd call 4x the BB out of position with Q 10, but he did. Other than obvious error of betting the river, I'm curious to hear how other people would have played this hand. Especially at this stage in a big MTT...