You are (or should be) psyched on the flop when your raise is reraised. I would put him on a set or a lower straight here (more likely a set). I would definitely say that you want to reraise all-in on the flop. If he folds (which he would have in this case), you take down a nice pot. If not, you are WAY ahead, holding the nuts and all.

Yes, you want to play with some caution when the board pairs. This was just a weird hand, I don't really know what the guy was doing but you were way ahead until the river. Given the range of hands that you can reasonably put him on raising you on that flop, I would generally be very cautious about the turn bet here...I would think that there are very few worse hands that can call your all-in there. But then, the rest of your stack is probably about half the pot at that point, so how much less can you really bet?

I think your problem is solved by reraising all-in on the flop.