I'd raise over him on the flop only if I haven't already taken some stacks with a c/r before.. in that case people know I mean it and I'm getting folds often. So imho it's preference. Usually I'll wait for the turn, like you did. But on the turn you really need to check/raise man! Especially with such a godly turn card for you.. he's not gonna be laying down a hand that just improved. Never

About the river.. you really need to fold here imho. But it's very understandable you called. I call here so often too, simply because I'm cursing the river card and I don't want to lay down my beautiful flopped set. I only manage to lay something like this down if I prepare myself for it beforehand.