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Kinect and MD5 skeleton alignment

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I'm working on a piece of software to deform an MD5 model using the Kinect skeleton. I've got the model skinned and running with animations so that side is looking good. I've also created the Kinect skeleton successfully in 3D using the distance between joints(bone length) and the relative rotation matrices. However I'm having abit of a problem getting the Kinect Skeleton to line up with the MD5 skeleton. There are two parts to the problem position and rotation.
First the positions used for bones in the MD5 format are they relative? Are they percentages or do they represent real coordinates in the joint local space?
The second question regards rotation I have joints that are basically wrapped around themselves (essentially over-rotated) is there a fix that would allow me to align the Kinect skeleton rotations with the MD5 model rotations? My current thoughts are to create offset rotation matrices to counter the rotation problem but that means each skeleton has to be manually calibrated.
The overall aim is to have the model move the same as the Kinect skeleton. I have examined the Avateering example for XNA however I find it difficult to follow clearly.

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