@Interesting (if I didn't list it, I don't know the answer):
2. Material only affects item quality in that it affects which skills you can use to create that item (for instance, a Bowyer can make crossbows only from wood while a Weapon smith can make them only from metal, and at the same skill level Bowyers make better crossbows).
2A.Yes, weight is a significant factor in how much damage an fired ammunition does. The densest materials make the best ammo. Keep in mind though, even the densest wood (Glumprong, 1.250g/cm^3) is only a fraction of the weight of the lightest metal you can make ammo out of besides Adamatine (Iron or Steel, 7.280g/cm^3). I'm not sure what effect hardness has.
3. You can find more than you ever wanted to know about stone
on the wiki. As for best wood and bone, I think all bones are functionally identical and the only factor separating different kinds of wood is density.
4A. They're something that has full value in any shop, as opposed to money, which only has full value in the civilization it's made by (anywhere else they'll only pay for the material it's made from).
4B. There's no magic at all in DF right now, and won't be for quite a while.
4C. Yes, clothing can block attacks like armor does but isn't nearly as good at it; generally cloth will only protect from small animal scratches. Leather is better, but still nowhere near as affective as metal. For more details see
this page.5. Bags are meant for storage and hauling not personal toting, the same for barrels and chest. You're right that you can't equip bags, only backpacks, quivers, and waterskins.
6. and 7. You can have multiple backpacks (either worn or within other backpacks), but it's not at all necessary: there's no limit to how much stuff you pick up off the ground you can fit in one, only to how much you can put in there from your hands (which no one really understands), which can be bypassed by simply dropping an item on the ground and picking up when your hands are full. And I guess you can fill a barrel with water (hit 'I' while next to some water and select the barrel), but there's not much point now in this version since hunger and thirst have been disabled.
9. Just make an offer ridiculous unreasonable in your favor (if you offer him anything ask for all his money even if you're asking for items more valuable than what you're trading, if you're only buying from him ask for everything for 1) and he'll counter with the minimum value you can pay.
10.
Yes, there are. If you have any questions that page didn't answer, ask someone else because I don't know much about those.
11. I don't think being covered in a material affects you unless it's poisonous, besides maybe weighing you down a very small amount. You can wash off yourself and all your gear by just swimming in some water for a few tiles (so long as you a good enough swimmer not to drown) and the water covering will eventually evaporate.
12. If their inventory is empty they get new items the second you sleep, wait with the sleep menu, or use quick-travel, though they never seem to get new money.
As far as I know shops are never robbed by anyone but adventurers.
I'm not sure if stuff you leave there remains your property, but I'm sure no one else will take it because NPCs never pick up items in this version.
13. No, you can't stack items at this point. The best solution is just to buy as many items as possible, exit the trade menu, pick them up, and then resell them.