Hi Larry,
Thanks for your question.

That's a very fascinating hand you are describing. With a dream flop like that you have two concerns: get paid as much as possible and avoid getting drawn out.

Slow playing might bring trouble
If it had been a rainbow flop I definitely think that you should slow play the hand, but with two spades on the board things get a bit more complicated. The problem if a third spade hits is that you might loose (obviously), but also that the action will slow down. With a raise on the flop you might scare some players of, but KQJ is a real action flop that several players might have a piece of (and many players won't lay down a two pair, or even AK, if you raise here.) Also (as you pointed out), its not only the flush that you worry about, a paired board might put you in an even harder spot.

Raise to protect your hand or get paid
I think a raise is in order here. You want to make your opponents pay to draw out on you and also build the pot with the best hand. If they fold - so be it. It's better than to be outdrawn, especially in a tournament where every lost chip is worth more than each that you win. So when your opponent bets out pot here, I think a raise of 2/3 of the pot to pot size is in order. (My guess is that his pot bet is about 600 chips, so you could raise to about 1,800 - 2,400. Putting about a fourth of your stack on the table.)

You could raise it up even more, to try to pot commit your opponent(s), but the chances that they fold will also increase. And if you do and get called, you'll have to go the whole way with your hand no matter what. What you really hope for is somebody putting in a re-raise, but if your opponents are decent it's not very likely on this flop. You don't mind the original raiser to call you, while the opponent behind is more trouble because of his position advantage (another reason to put in a raise.)

The turn
If the turn card is a blank, you can definitely go all-in (there will be at least 5,000 in the pot and you'll have 7,500 left at the most). If the flush card hits or the board pairs it's a different story. But if you've got the second opponent to fold you'll at least have the position advantage. If you raised more than the pot on the flop you'll have a sure all-in, especially with a re-draw to the nut flush.

What actually happened
Let's look at how the actual hand played out. When the third flush card hits on the turn I think you make the correct decision to just call the 500 with your straight and nut flush re-draw. I am not sure about your stop bet on the river, it both have positive and negative effects. The other solution would be to try to induce a bluff and check call. Because there is a large risk that a stop bet won't work against a player holding a flush (even though it's not the nut flush).

By checking you might make get the player behind to make a final stab at the pot and if you are lucky the other opponent will call. The downside to this is that you might be forced to make a much tougher decision if the player in last position puts in a substantial bet (like you said). And you might be forced to pay off someone with a flush. (But you'll have a pretty tough decision if your stop bet gets raised also.)

Conclusion
Your dream flop can prove to be quite dangerous and it's a good idea to try to protect your hand. You also want to get as much in on the flop, before a scare card might cool of the action or force you to make very tough decisions. If you play the hand hard on the flop you force your opponents to make the tough decisions instead.

Sorry about the long answer. ;-)
But as you said - it's an interesting hand.