did i make the right call

[samdar]

I was in a MTT and there where 14 people left. I have just doubled up to be the 6th largest stack, 3rd at my table. Blinds are at 1000, 2000 my stack is ~34000 big stack is ~82000

I am on the button and get pocket nines. The #1 stack is first to act and calls the pot. I raise 5k on the button and only the big stack calls. Flop is
4c 6c 8h
I raise 2k
get called
turn is 9s giving me the set
I push (figuring that in first position he had 2 over cards)
he calls
flip our cards he holds Qc 3c
I show my set
River comes kc and he wins with the flush

looking back I figure even though I hit the set there was a straigh and flush draw on the board so I was in danger.

I figured if I double up off the #1 I would be close to the #1 and make it into the good money.

Did I make the right call or should I have folded?