Having a hard time deciphering all this. It sounds like you were fairly early in the tourney? I think Philthy gave you some mathemetical reasons that you can justify a call, but I would probably fold. I don't want to go out of a tourney early chasing a flush or straight. Plus its not out of the question that he could have something like the Kd/Jd or even Ad/Jd, which would also give him potential straight draws and counterfeit your flush draw. A jack would give you a straight, but what if he has AK? It also completes his higher straight. And a diamond would give you a flush, but again, if has two diamonds, including the ace, he would have the higher flush.
You have to look at a tournament like a marathon. You're not going to win it in the first mile. You have to just hang on through for most of the race, and then put it in high gear over the final two miles.
It sounds like you are playing in a Pub Poker League tourney (Steel City Poker?). I play in the local league in my area (Atlantic Poker Tour). I had a similar situation last night in our league. Each player starts out with 20,000 chips. After the first 45 minutes, I was down to about 15,000. I won only one hand in the first hour. For the next hour, my stack stayed between 11,000 and 19,000. I could not get anything going. When my stack was about 16,000 I flopped a nut-flush draw (I had K-Q spades) but my opponent shoved me all-in (he was first to act after the flop). Since the Ace of spades was on the board, I was fairly certain he had an ace (he flipped it over to confirm - nice of him). I had about 12 BBs left. I know that a lot of people would say I should have called, but I decided not to chase.
A few
hands later, with my stack size still the same, I got KK and raised it up to 4,000 preflop, getting one caller. The flop came up Q-9-6 rainbow and my opponent (again first to act) shoved all in. I called, and he flipped over Q-J. I survived the runout and got a much-needed double up to more than 30,000 chips. That put me back in business and I eventually won the tournament. Who knows what would have happened if I chased that flush earlier? If I don't get it, I'm out.
This gets back to my philosophy that it is better to fold a winner than play a loser, especially early in tournaments.