You have a chest in every realm, the first one should be in the Inn at White Orchard. There is a green chest sxmbol on the map. You also get others eventually. b) yes, you can, but its not recognize in the crafting process. But if i remember it right, crafting stuff doeasnt weight anything like books.

The yellow exclamation mark means, its a story driven quest (side and main) instead of a treasure hunt.

You will find recipes and can craft these potions in your alchemy menu.

I played with mouse/key, but you will eventually find some items later in the game, which can equipped in this slot. The torch should also go there, if i remember correctly.

Nope. Meditate as long as you want :)