I've been running a reanimating fort for a few weeks now under 44.05, so I can clarify a few points.
1. Corpses and body parts will reanimate unless they're mangled or mutilated. I had problems getting bodies into coffins, but that was probably from a bug unrelated to the reanimation.
2. I've been using maces on the undead, and they seem to mangle just fine. Once the undead go down, they don't come up again, at least with maces.
3. Butchering is tricky. Hair, wool, and skin will reanimate and disrupt your workers. They aren't dangerous, though. I've never seen one injure a dwarf. But, they can cause a morale hit if your butchering area is in sight of many dwarves. Once a battle starts, all dwarves in sight will join it and gain a "vengeful" hit to stress. So butchering works just fine, as long as you don't mind a few interruptions and keep it out of sight.
4. Undead have plenty of useable parts on them, so don't forget to butcher them. You could even think of caging undead grazers as a superior alternative to pasturing live ones.
5. On my map, the surface-level wildlife spawns as undead while the cavern wildlife spawns normally. But creatures in the caverns fight and generate corpses, which reanimate. After a few years I had hundreds of undead in my caverns, who swarmed and killed anything that appeared, including FBs. And so the horde grew. Opening a cavern at ground level is not to be done lightly. While the surface undead only attack on sight, the cavern undead all sensed the path to my fortress and took it immediately. An undead horde in a sealed cavern probably drains your FPS a little, but an undead horde in an open cavern will drive your FPS down to single digits.
6. Reanimation takes a random amount of time, so don't assume that the dead will just hop up and fight when you want them to. I had to wait nearly a month for a cyclops to reanimate and walk into my cage trap.
7. Armor works great against the undead, because they mostly just scratch and bite. I put all my dwarves, except a few miners, into squads with full armor.
8. Caravans are vulnerable to surface undead, because guards armed with bows or spears are useless. I tried letting the caravans walk over the surface, but it failed too many times, and I ended up building a caravan tunnel.
9. Undead make awesome training dummies for marksdwarves. But then, marksdwarves are useless against undead.
10. Undead are all on the same team, and I believe that they're hostile to HFS. And the dead are immune to syndromes. I'm planning a huge battle of HFS vs Army of the Dead. Stay tuned.