How to reliably hurt dwarves without killing them

Well, it's kind of tough. First, meditate upon the Constructions page on the magmawiki. This may explain some other problems you'll encounter soon.

Your specific problem is caused by having no stairs on the second level of your tower. Remember that ordinary dug stairs only work if you have a "down stair" directly above an "up stair". Constructed stairs work the same way. The only square your dwarves can reach is the one directly above the stairway. In this square, on the second level, you need to b-Construct a down stairway or an xup-down stairway. After this your dwarves will be able to get to the top of the first-level walls (which come with built-in floors above them; do not build more floors on top of them because it will prevent you building walls instead). I recommend building a floor on the interior of your tower before extending the walls upward, and remember to build the corners first.

Ok, I am going to attempt to answer all of your questions one at a time.

First of all, you wondered about clothing and arming your dwarves. While is does become a problem at some point, it doesn't usually for a while, you have at least enough time to buy cloth from the merchants (they always come with a ton) and build a couple workshops. Arms-wise, you should only have weapons in use by your military, and you shouldn't need a ton of military dwarves, it is always most efficient to have your defenses based around traps.

Secondly: bedrooms. I have found that it is best (until you reach the population cap, although that tends to be a bit buggy) to have all of your dwarves sleep in one giant dormitory with many beds. You can do this by building a bedroom that encompasses all of the beds in the area and then toggling "dormitory" to "Y." This way, you have one area where all of your dwarves sleep, and the only thing you will need to worry about is having enough beds. You probably only need the number of beds to be 25% of the number of dwarves you have, as that should cover all the sleeping dwarves. It is even better to have a much larger room with half of it being a statue garden, as then you will have dwarves in the room who are awake and will see it if any vampires start killing dwarves.

For pens and pastures, there isn't a great way to make them efficient that I have found. There isn't really a great need to have them, though, because you can buy a lot of cheese and cloth from merchants. The only reason you would need a pasture, I've found, is for a chicken egg-laying area, but for that, you can make it underground in stone, you just need to be sure to have nest-boxes.

Building configuration-wise, I find that it is good to have a set plan for design before-hand. For example, know that you will put a lot of your workshops in one area, and your meeting hall and bedroom (see above) in another. It's also good practice to only dig out enough room for the workshop and not to group them all together in one room. You should also have rooms for your stockpiles near the corresponding workshops. Also be sure to have one "main" hallway, it should be 3-wide or more, as this will prevent traffic jams down the road.

Finally: farms. I would recommend you build a couple plump-helmet farms, as large as possible, to feed your dwarves. Seeds shouldn't be a problem, just go to the overview (z) menu, move over to kitchen, and disable plump helmets for cooking but not for brewing. You should have several breweries to make alcohol, and these will also return seeds. It is also good to have an egg-laying center (see above) and a kitchen. Hens and roosters will produce a ton of eggs, and if you set your kitchen to auto-repeat cooking easy meals, you should be able to feed your dwarves.