They're rare harvesting materials... I have a few they go fairly well in the Bazaar ... they're pretty rare... I haven't seen any notes about it but it seems like they increased the drop rates of Materials off regular Mobs, and Bosses.
Ore is around Dragonspyre. I went back to Krokotopia and farmed Ore in various zones there. My favorites were Champer of Fire, palace of Fire and the barracks in Tomb of Storm.
You need to go back to recipe vendors and see what recipes they have for turning some of your reagents you have into the needed items. Especially go back to Marleybone and Mooshu. Myself, I went to every recipe vendor and bought every transmutate spell they had. :)
If I remember correctly, sometimes diamonds drop in piles of Ore, and Ore can be transmuted into diamonds.
Black lotus is from Mooshu and I found the Tametsu village the best place to farm this. Try to get on during a time when it is not so busy. This takes a lot of running around. Sometimes a rare black pearl will also be picked up with black lotus.
You will find you need red mandrake in a later task. I spent a lot of gold on this at the bazaar since finding it was harder.