I keep making floors. They are pretty. I read somewhere that dwarves dont care what the floor is made out of. Considering the pain of filling rooms with objects with floors (since you can't just square select and it will "use" the available spots for floor) this seems a bit weird. Should I just stop making floors? I want to focus on a functional fortress.
Floors are rarely worth it. They barely affect room value, are a pain to designate, and take up all of your masonry force. Unless you've got a lot of gold laying around, don't bother.
Smoothing, however, is great. All the benefits of a floor, but it's easier, doesn't use the masonry labor, and can be turned into a (possibly) valuable engraving. That only works on stone, though, not clay, sand, etc.
1) Just keep digging. You'll find Fun stuff eventually. I use a 2x1 up/down stairwell designated 10 levels at a time. It goes pretty fast.
2) Silver warhammers are one of the best weapons you can have. If you don't have ready access to steel, keep with those.
3) Doesn't matter. They're terribly uncontrollable no matter what way you do it. Try out different methods and see which you think works the best.
4) I use quantum stockpiling for stone all the time. It's easy, and I think it's pretty reasonable. Alternatively, you can hide it with d-b-h, if visuals are your problem.
5) "Prettiness" is rarely a factor in my fortresses. Dwarves don't really care about the clay until it's in their rooms or dining hall. Digging and replacing with stone just looks worse. Keep digging, relocate your living areas into a stone layer. Move into the caverns if you must.
6) Dig down or wall him in. If you don't mind losing a tanner, the easiest solution is to kill him (or, rather, lock him up and let him die). There's no guarantee you'll find spider silk.