[phish]

I think there is a very good chance you got bluffed. I've played w/ John a lot, and the fact that you say he likes to three bet or call your raises means he thinks he can often play you off hands.
There is a good chance that he only had JT, and no flush. If he had AK or AQ he likely would have 3-bet pre-flop. JT sounds like a likely call hand for him in this situation. There's a chance he may've made a flush, but the pot is certainly big enough to call the river on your part. Do you often go to the river in situations like this and then fold for one more bet? If you do, I can guarantee he would've picked up on it.
Much of your post talked about how you've been playing pre-flop (raising w/ solid hands), but never talked about how you were playing post-flop. Frankly, for expert players, how your opponent plays post-flop is much more important. And playing too tight (folding too easily) post-flop is, when up against someone like jdag, a more costly tendency in the long run than calling too much.