Questions about some items post-Chaos

and I take it graded gems and crystals are worthless too?
How about PoT what does it get used for later?
Does anyone have a link to how these professions work, how often you may use them, how you use them, etc?

Yes, graded gems are useless. PoT's are still used to craft Reverse items. And the professions are just am optional thing to the game, much like maker, it does not affect gameplay, but enhancing it instead. It also affects your personality traits.