You forgot to mention Burrows and Military Alerts. That's how you keep people inside during combat. Look these up on the wiki.
I know...
But unless you know there is an ambush the allert is offline. Otherwise you have to change the burrows everytime you expand your fortress. And if there is an ambush the goblins usually appear next to a dwarf or an animal next to a dwarf.
Huh? WTF you're not making sense here, it's not as compilcated as you make it out. Siege comes, put alert out, guys stay inside. Siege over, cancel alert. It's like 3-4 keypresses to activate. You only need one safe-area, though it's nice if it includes your workshops etc. A guy outside who gets fragged isn't savable anyway. Anyway you do NOT need to expand burrows every time the fortress expands, you can burrow entire z-levels before they are dug out, i'm pretty certain.
And if your not letting guys outside (eg the alert is on 24/7) then you'd just lock the front door, not use burrows. Alerts are for areas which need to be regularly accessed (eg surface for woodchopping), but you might need to keep people out of at some point.
Say you use cage traps, Burrows/Alerts stops the dwarves trying to refill traps or haul caged gobbos in while the siege is still on.
Also, do you declare zones as water sources?
Oh, and BONE BOLTS, a use for your bone carver, and you never need wood for archery.
If you have a river, automated goblin drowning is easy to design, no cages required.
For the danger room, forget pressure-plates. Make the room smaller, and 100% traps. Lever outside, set it to be pulled constantly with q-a-P-r, and an idle dwarf will keep pulling the lever. Alternatively, link the traps to a repeater like on the wiki. You probably set the pressure plate to "activate by creatures" rather than "activate by citizens".
As for military grade metals, Silver makes great hammers and crossbows i hear. Use copper/bronze armour with this until you get some iron/steel.
You should really look at the very simple measures to stop enemy access :-
H = Hatch
P = Pressure Plate
H = Hatch
in a thin tunnel, will stop pretty much anything, just set it to "creatures" and the widest weight range. your dwarves will still pass like normal. You may only need one hatch, depending on which side the enemy are coming from, but HPH will stop enemies going either way.
You can make a room with many small entrances with HP combos in each (don't forget to channel, remove ramps, under the hatches). Enemies can path into the area, but not path out, or escape in any way. Once there's a bunch of enemies trapped in one, you can take them out anyway you like, eg turn it into a drowning chamber, or have a wall (well, a raising bridge really) which comes down to reveal marksdwarves behind fortifications.
Or like others said just have a hatch over some down-stairs leading to the outside, and it's as good as the best defence ever. Takes like 3 seconds to set up.