When I said "I would have won with 2 pair" I didn't mean I should have played it through, just that in that situation you at least want to see someone win with the straight or the flush, or even Aces over something, BUT NOT A PAIR!!!
I agree you CAN NOT chase in these situations or you will find yourself on serios tilt when they get better results from their chasing (like you said losing to A9).
Edit: Do you mean chasing it as far as I did, or that I shouldn't have chased it any farther. You are probably right in either case. If you think I should have folded on the flop, what situations might I stay in the hand in your opinion? Only with a open ended straight draw, flush draw, or two low pair? Obviously, top pair (with good kicker) and better I would play back into him.