1) Farming was changed around so that it takes a lot for everything to grow. It looks like crops take at least a full season to grow. The crop yield is dependent on the level of the Farming skill. The higher the skill, the more likely that you'll get a larger stack when harvest time comes.
2) Cave wheat and sweet pods in their natural forms are inedible. They can be milled at a quern (requires the Milling labor) (built from the Mason workshop) to procure flour and sugar respectively. Those can then be cooked in a Kitchen (with the Cooking skill.)
These can also be brewed in the Still workshop, with the Brewing labor, along with plump helmets and Pig tails. Pig tails are otherwise inedible, and are used in a Farmer's Workshop (process plants) to make pig tail thread.
Quarry bushes must be processed into a bag (which must be empty beforehand). It also requires the plant processing labor at the Farmer's Workshop. Each unit of quarry bush will yield a stack of 5 quarry bush leaves.
3) Designate a zone (i) that has grass. Then designate that zone as a pe(n). Then desig(N)ate which animals will go to that pen.
4) Create a Butcher shop near the refuse pile. Make sure the Butcher labor is enabled. There might also be a point where the corpse becomes too rotten to be butchered even though it might not say so. (There's also a possible matter of how it was killed, but I'm unclear on that aspect.)
5) Harvesting fish requires the Fishery workshop and the Fish Cleaning labor.
6) Hunters will stalk a target and (try to) kill it. I'm not sure about capturing, haven't played around with either of those.
7) Aquifers can be a lot of fun, but I'd advise using an aboveground source of water, like a brook or a stream, while you're learning the ropes. Then again, Losing is Fun!

You'll want pumps (one enormous screw, one block, one pipe section for each pump) which can be built from the (M)achine selection. Make sure that you've got some place for all that water you'll be pumping out. You'll need the Pump Operating labor enabled to use them. To plug the aquifer, you'll need to build walls around the dig site. This is easier when the aquifer is in a stone layer since all you'll need to do is d-(s)mooth the stone.
To access that layer, you could build ramps or a set of staircases. Constructing those can be done from the b-(C)onstructions menu.
Another option, one that I've no experience with as yet, is to construct walls (and staircase) above where you want to punch into the aquifer. Dig the area out (channeling works well to keep the dwarves dry) and collapse the constructed walls into the aquifer layer.