I'm not a Masterwork player, but I'll give my 2 cents on the non-Masterwork stuff.
Farmers will often be idle for a while in my forts too. I usually make one of my starting seven do pretty much anything remotely farming related, and then let migrants be more specialized. I find planting a relatively high priority task. If your farmers can't keep up, then maybe the farmers need to have less other jobs. Or maybe your farms are too big, or you may simply need more farmers. It doesn't sound like you are "terribly wrong", it just may need some tweaking.
Water falling doesn't generate much mist until it hits bottom. Probably the best mist generator is to have a circle of pumps above where you want the mist to be. See the wiki
mist page for a description.
Unfortunately, you can't specify the material of the bins in a stockpile. You'll have to either be careful when trading with Elves, or not trade the bins away.
Kilns can also create bricks (in addition to trade goods and furniture), but really are optional. Pots made from fire clay (or other types of clay once they have been glazed) can be used as alternatives to barrels too. The only thing that absolutely needs a kiln is baking potash into pearlash - which is used in making clear glass or crystal glass (green glass doesn't need it). I assume clay ovens are Masterwork specific.
The initial training of a wild animal changes them to "trained" (or "-trained-" or "*trained*" etc), but that will slowly wear off, going to "semi-wild", and eventually completely wild. Unless the animal is still in a cage, animal trainers will keep re-training them so that they stay "trained". But, if your fort is not good at training that type of animal, they may not get trained fast enough, and the animal may go wild on you. Caged animals are slightly different: they get "trained" like uncaged animals, but are never re-trained until they have gone completely wild. They are safer that way though, so some people like to keep animals in cages until the experience for that type has gone up. Babies of trained animals get the same training level as their mother. But, if you train them once, they will go all the way to "tame", and "tame" animals never lose their training.
In addition, some animals can be trained for war and/or hunting. That is a permanent (and quick) change.
So, all of that affects whether you want to assign a trained animal to the military or not. The other consideration is that assigning an animal to a soldier makes it that soldier's pet, giving good thoughts, unless it dies (giving very bad thoughts).
The easiest way to get an animal (or anything else non-Dwarf) out of a cage is to assign them to a pit zone. Dig a 1 z-level channel somewhere, and create a pit zone next to the hole. "P" to assign creatures to the pit; they will be taken out of the cage and put in the pit, and then they will wander off by themselves. (Dwarves in a cage -- like captured Dwarf Zombies, or caravan guards, or your own that fall asleep on a cage trap -- have to be released the "hard way".)
Mass dumping has been around for a while now (4 years? maybe more). In the old days, after a goblin siege, you would have to "k" over to a dead goblin, "d" to mark his iron helm for dumping, "+" to move down to his iron breastplate, "d" to mark that, "+" again, "d" again, "+", "d", etc, for every goblin. With mass dumping, you can now "d" - "b" - "d" and mark a whole area -- everything in the area gets marked for dumping. (The same thing goes with un-forbidding and mass un-forbidding.)
What kind of items are showing up in the stockpile menu, but not in the military menu? One possibility could be that they are foreign items (items your civilization can't make), those all show up at the bottom of the list. Everything else *should* be there to select as part of the uniform, even if you don't have any of the particular item at the time.
As far as the fort goes, I think that is a pretty interesting design. It should be pretty efficient, and would probably work very well. That being said, I personally wouldn't do it because it would feel like too much micro-management for me. My own population management is usually very loose: I let Dwarves wander wherever they need to, and use Dwarf Therapist to manage the jobs when needed.
But, don't let that stop your plan, go for it! I'm interested to see how well it works out for you.
"Same old booze" can be countered with even just two types of booze. So if you have tons of Dwarven Wine, you could do one stockpile that takes any booze except Dwarven Wine, and another (probably smaller) one that takes only Dwarven Wine. Then you would be pretty much guaranteed to have multiple types of booze on that level without needing lots of small stockpiles. (If you don't have excess of one type of booze, it should work well with other splits too, like one pile with Dwarven Wine, Dwarven Beer, and Strawberry wine, and the other pile with Dwarven Rum, Dwarven Ale, and Prickleberry wine.)
You are right about the small stockpiles not sharing with each other, so smaller ones are probably better in your kind of setup. Just be aware that it will create a lot of hauling jobs to refill the multiple stockpiles.