Yeah, most reliable way would be to cause rot in muscle/skin only, and via modding for science.
You would have to get super lucky in vanilla fort mode no matter how you arranged it, unless you had hyper-precise dwarf trick machinery going.
Not muscle, just skin and fat. Joints are made of muscle and are internal. Maybe you could do muscle if you had a localized contact rotting poison, then coated the whole dwarf with it? Needs science.
So the first syndrome can take out fat/skin, and then a second, doused liquid version that evaporates quickly and is contact only. A long process, but potentially successful.
Just sort of erode the dwarf until it is a skeleton. Are motor nerves kept in muscles?
It is probably possible to control the temperature of a body of water reliably using magma, pumps and some vessel with a high heat capacity. The idea would be to control the temperature of the vessel by exposing it to magma and then pumping it away again before it equlibrates, thus only reaching the desired temperature. Just looking briefly at the wiki, lignite takes about 500 ticks to reach magma temperature.
Maybe we can heat and then quench a dwarf rapidly until the outer layers melt away. There might even be a way to set up a machine that has exactly the required duty cycle to maintain a nearly constant temperature in the heat bath.
Thoughts?
Edit: On second thought it's probably better to use lard or fat which would have a broader liquid temperature range.
Edit2: Looking at the raws just now, skin doesn't have any melting point, but fat does, so although we can't use the above method to remove the skin, it's probably possible to remove the fat. Skin has [HEATDAM_POINT:10250], whereas fat has [MELTING_POINT:10078], so it even looks like you could melt fat without damaging skin. What happens if you do that?