Regarding "extra" bones that are not tied to a polygon group: very important to remember that any bone can only cause deformation it polys that belong to its own group (same internal name) and its parent group.  If you have a structure of Bone1 with polygon group, Bone2 that is a child of Bone1 and has no polygon group, and Bone3 that is a child of Bone2, this will cause problems - Bone3 will not cause any deformation in Bone1's polys, and even if you have a poly group for Bone3, moving that bone will cause a break in the mesh.  This may be OK for machine moving parts, but not OK for organics or clothing (usually).

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