Sorry for the late response. It happens during the weight painting step.
Also, what is the best way to get as close to the mannequins rigs as possible? I rigged my character up and everything looks fine but retargetting from Kubold’s animations (which use the UE4 Mannequin) are a bit off. Is the lack of IK foot and hand bones the result of this? Or is it because my model has different enough proportions in certain areas to have problems. Clavicle, wrists, and arms seem to be problem areas.
I have followed the Retargetting tutorials, and documentations, but only found slight fixes.
What is it that makes this skeleton completely different from the ue4 mannequin one btw? The bone names and hierarchy seems identical.