Misplayed Every Street?

Preflop: Raising will generally make 99 easier to play. If you are open limping, you better have a very good reason for doing so.

Flop: you shouldn't be folding here. At this point the CO can have a wide range of hands. I am not sure why you would 3 bet here. He is only folding hands that you beat, and he probably isn't folding high cards.

A preflop raise would make things easier, but you still wouldn't have had easy decisions postflop.