I think you played it fine - the push from villian #1 is most likely either a made hand trying to protect from the flush draw or the nut draw or some combo of the two (and since it was a limped pot the made hand could be a set or 2s or 3s or literally any 2 pair or top pair w/ a spade) - minimally you have to call. I like the push in that it prices out Villian #2 if he called w/ the nut draw. I would have been shocked to see Villian #1 turn over a hand that beat yours and you were just unlucky Villian #2 flopped the nuts. The vast majority of the time you pick up 3000 chips from Villian #1 (although I wouldn't have had Q w/ 9s in my range for him).