I think I have a pretty decent solution for the joint orientation, however I 
notice some flipping of the axis in some instances.

my method is to get the xyz coord from the endpoints of the edge and then 
calculate the rotation value from that.  since i only have 2 points, and I need 
3 i set the 3rd point to (0,0,0) but I think thats not a good way, im not sure 
what the best way to define the third point for the YUP axis.

here is the code.
http://pastebin.com/DYck03Cj

here is a test maya scene
http://pastebin.com/XRt06bCZ

it works pretty well but you can see around the corner the joint axis flips so 
instead of flipping down they flip up.

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