you've gone very long with your bedrooms. What I tend to do is go wide and deep. I build a long hallway, 2 wide. and I put branches 7 rooms wide on each side. If you also put stairs at the front of this area, you can house all your dwarves in rooms, and keep them very close to the production area, so they don't need to travel so far to sleep.
Keep in mind though that if they are within 20 tiles (IIRC) of workshops they will be "bothered by noise" when they sleep, which will give them a negative thought. If they all have masterwork bedrooms that can offset it, but I still tend to dig in the opposite direction of the workshops and a level above or below to keep them from getting negative thoughts at all. Also give everyone a cabinet to put their claimed items in along with their bed or you will wind up with claimed crap all over the ground. You don't need very large rooms, since they will be happy with a nice bed and cabinet and size of bedroom doesn't really matter. (Except for nobles - make 'em big and put expensive crap in 'em.)
http://mkv25.net/dfma/map-10310-diamondrelicI'm a couple years past this export, but haven't done much construction since. You can see where I've built my bedrooms. (on level 36 - the map viewer seems to drop you in random places all the time.) Workshops are on levels 39 and 41. Travel is still fast and convenient via the central ramp system.
I use ramps rather than stairways - a ramp counts as one step to go between levels but stairs require 3, I think. One to step on the stairs, one to move up/down the stairs and one to step off the stairs. They can also lead to congestion since only one dwarf can use it at a time so they have to wait while another dwarf is on them.
I make my dorfs walk through an "outside" area if they go to or leave from their meeting area. And I station my military dorfs outside on station one season a year for the same reason. So far I've pretty much avoided cave adaptation on anyone by doing this. It keeps them from getting pissed off if they have to go outside.
Use burrows - use the link boyhowdy posted and learn it well. Burrows are a necessity for both military action and keeping your civilian dorfs inside when there is an ambush or siege.
Set up traps. Stonefall traps are fine for the first year or two. Once you get metals, set up weapon traps. A masterwork mechanism with a handful of captured weapons will turn invaders into kibble quickly and easily. You could also set up cage traps so you have prisoners for your military to practice against.
All of those refuse piles consist solely of the skeletons and skulls of dispatched enemies. My military is pretty badass.
![Cheesy :D](http://97.107.128.126/smf/Smileys/aaron/cheesy.gif)