Hello Lee,
You should define the subjects’ height and weight, and additionally include the code outlined in Tutorial 15: Personalize Your Model (Lesson 2). Yes the source femur STL should be the non-scaled femur (the TLEM 2.0 cadaver bone geometry in the local coordinate system). Then your target femur needs to have the same topology as this bone, this thread may be helpful (https://forum.anyscript.org/t/patient-specific-model-with-mocap-model/2688/10).
Best Regards,
Christine