99 overpair out of position on $100NL 6max

[jacknine]

I got myself into a nasty situation on Stars $100NL 6 max and wonder how I could have avoided it...

Villain has had a lot of comments from other players about playing terribly. From what I've seen, this guy is tricky, cleverly mixing up his play. Looks to me like he knows what he's doing.

me: $120
villain: $260

I'm in MP holding two black nines.
Folded to me, I make the standard 4x BB opening raise.
Dealer calls, all others fold.

Flop comes 3 6 4 rainbow.

Apart from hitting the set, I suppose this is the best flop I could wish for. I bet the pot because I want to take it down right there. Villain calls.

Turn pairs the 4 on the board. Two diamonds.

All of a sudden I don't like the situation anymore. Me out of position with my med.overpair against a tricky villain who smooth called my bets for a descent sized pot. As always I ask myself - how did I get into this mess?

1). should I have merely limped preflop?
2). was my flop bet wrong?