I could only check your code lightly, but if the rope example is working correctly, it should apply to any skinned mesh.
You can load and check the bone structure (of the rope object) with Fragmotion, and you should study the complete rope sample code. The order of ragdoll parts assignment is important.
Why do you use fixed joints? Do you want it to be stiff as a corpse? with fixed joints it will act as if you crazy-glued-solid all body joints, so it is no mistery why it does not looks natural. For sure it will plummet like frozen. A ragdoll should use spherical or revolute joints in the first place.
Try changing the joint type, for starters.
As for the incorrect skin deformation, since "Aiko" is a tested and working model, probably you are missing some bone, so when running the simulation, the model deforms, but not the one you missed. It probably stays on mid-air while all the rest follows the simulation. (I say "probably", because remember I have not inspected entirely your code)
This sounds just like what usually happens with vertices when you are making a model and you rig (skin) a model and fail to assign or weight one or more vertices correctly, and the skin deformation is incorrect. Since Aiko is correctly skinned, you can only blame your ragdoll assignment for any incorrect simulation.
I suggest you take a video capture with "Fraps" and post it to YouTube so we can see what is happening on your screen.
May the 3d force B with U