Actually, if you want to produce bones, an indoor (or, more accurately, underground) refuse stockpile is what you want. Bones and skulls will eventually disappear if they're outside, but will stick around permanently if indoors. Of course, all those limbs and such will produce miasma indoors, so you might want to create 2 refuse stockpiles, one outdoors that specifically doesn't accept fresh raw hides, bones, skulls, or shells, and a second indoors that accepts bones, skulls, and shells.
Also, you might find it beneficial to make 2 or more bridges in your animal-pen-pit things, so you can drop and kill only part of your herd rather than the whole thing. Finally, while a long drop is the most efficient means of killing the animals, I believe that if you want meat and fat from them you have to actually butcher them, so dropping them only 1 level and then having your butcher go to town might be more desirable.
For the secure woodcutting area, I would suggest digging the drymoat first, but then building a wall around the area as well as soon as practical. Bowgoblins will still shoot over the moat, so while the drymoat reduces ambush risk by about 90% it doesn't totally remove it. Also, crossbows are about the most dangerous things goblins can wield anyway, so protecting against them with a wall is very helpful.
Finally, you might want to develop a path, carefully controlled with doors, hatches, and/or screw pumps, to collect rainwater as it falls into your murky pools and direct it into a subterranean cistern. Underground pools have a lot of water in them, true, but if your fort runs long enough you can still run it dry.