I think if you cut the model, named it appropriately and gave it the correct JPs -- making it just a regular old conforming figure rather than worrying about seperate IK chains and such -- I think you would end up with much better results than you think. When you create a conforming figure you have to cut it and set up the JP's in such a way that each part moves correctly in relationship to the figure, rather than moving correctly in relationship to its other parts.

Hope this helps.