Hand 1: I believe you played this hand fine. Nothing looks off the wall.

Hand 2: I might be on my own here, but I think this is a clear cut fold. You have 13 outs, (3 J's, 3 9's, 3 T's, 4 6's) and are around 3.5-1 to hit your hand.

The pot is laying you 2-1. Unless you feel that you will stack him everytime you hit, I would lay it down. (did not even mention that a few of your outs will most likley be in his hand)

On the turn, you are presented with a similar situation, only some of your outs are not to the nuts anymore, due to the flush. I would lay it down again on the turn. On the river, obviously, its an insta-call.