That's good to hear.The plants grow after you have entered a dungeon or a room you also can just save the game and load your save.The new Equipment's are droped by enemies.
Okay then now though I have to try farming exp to get strong enough to fight the Root guardians I got to one in the sewer and well it killed me quickly. I have found I can have Bunshido help me fight the Bandit boss to farm him while in passive mode as otherwise Bandit boss creams us both but is there any other fight I can do to get lots of exp from? And yes I have been getting the superior crystals to get more from bosses. And I guess to get seeds I just fight enemies and try to get the ones i want?