I think the river bet is fine, but when he raises you need to fold.  It's not like he's ever bluffing, nor does he value raise a worse hand.  You're beat 100% of the time, so just fold and know you made the best play possible.

First things first, betting the river is completely mandatory and your sizing is fine - his range mainly consists of missed draws and aces up (sometimes the missed draw can be nut diamonds which may have two pair also). Against those hands, you don't get anything from the draws and the two pairs will probably call a decently large bet (if they are willing to call anything bigger than a tiny one) so a small one seems stupid to me. If anything, I might have gone slightly larger, but $41 into $67 is fine.

As for how you should play this following his raise, I think it's kinda close. On the one hand, this doesn't look like it'll be a bluff, but on the other we do have the second nuts and I think it's possible he does this w/ some other stuff depending on villain (QQ + diamonds, 67, maybe even AQ). If he'd gone larger it would be an easy fold, but at the price we're getting I'm not wholly convinced tossing this away is our best play, especially given JT didn't have a draw on the flop which reduces its frequency somewhat (although he can easily have it along w/ diamonds, an A etc.).

You say you just have 90 hands, but that's often more than enough to get the info I'd want to make a confident decision here. He must have reached a few showdowns and knowing what those hands looked like would help a lot.