I discovered that it is possible to add both extra links and extra bones without any detremental effects. However, with the exaggerated biped deformation, I came across a problem that hadn't been that obvious on Knute and Bolte. most weapons are rigid non-deformable objects, however the Egon reference model is actually physiqued to a humanoid biped the same way as the player model mesh is. This means that when you deform the biped, it will in turn deform the Egon. It is possible to adjust the Egon model to fit Yodan, but that would mean including the altered Egon gun with the model which would replace the standard one. It would then screw up on standard models, defeating the whole point.
Beyond this, I feel the lupine legs and tail work quite well, though I realised that the legs are allready quite 'crouched' in the standing position which didn't leave much room for actual crouching =( However, the root Bip 01 bone is in the same place as the standard Human ones when standing and crouching.
I have totally re-animated all of the sequences, but largely based those animations on the Valve ones so no points for originality. However, I have made him fire most weapons, including the missile launcher one-handed, I felt it kind of suited him =)