1. Bones are retrieved only from "naturally butchered" arms and legs, with whole (including mangled, etc.) corpses not yielding anything. Thus, to gain such parts at larger scales you need something to remove those body parts from their (previous) owners, such as with weapon traps or splatterers (drop the victims from a sufficiently high elevation to cause them to splatter when hitting the ground [preferably something heavy, such as lead or, the ultimate, Slade]). Also note that "naturally butchered" bone from former sapients that were undead when the butchering happened does not count as bone from sapients from a crafting perspective: dorfs will happily make dwarf bone greaves from such bones.
4. If I remember correctly, negative numbers are the bad ones. The extreme end is -100000, and they'll get into depression/tantruming/... well before that, although mooding makes dorfs immune to insanity itself, but certainly not the depression, etc. When your dorfs get yellow exclamation marks over them they're starting to get stressed.
5. While migrants often come in (partial) family units, I don't believe I've ever seen any relatives of anyone arrive in subsequent migrant waves, but I mostly play so I get void dorfs as migrants... I believe the pop cap includes the whole population of the fortress, i.e. everyone except visitors (diplomats, merchants, etc. are visitors for this purpose), so it counts residents and adult and child citizens.
Given that dorfs get stressed from being separated from loved ones when they don't have any family at all to be separated from (and effectively being incapable of creating one though courtship), I think not migrating with the whole family is a lesser issue, especially if the non migrating ones have a good reason for not being able/willing to migrate.
6. Not without draining the water. You can drain a murky pool with a bucket brigade or with screw pumps. A screw pump can also remove sufficient water to allow dorfs access to a tile even when there is 7/7 water in neighboring tiles, but logs can float around and create a danger (and flowing water is a danger in itself, as it can sweep dorfs away). To pick something up dorfs have to stand int the tile, so the water level has to be decreased to 3/7 for them to enter it.