If I recall correctly, seelct the armature chain and then go into EDIT mode with TAB key. Then select all with A and then press CTRL+N to get all the bones raxis reoriented.
Why not simply add another link in the Armature chain to round it off. Thats what I would do.
Or theres always weight painting…its in the Object Mode drop down menu, its the dog bone with the red square behind it. The blue means no influence and the red means full influence. If you want to remove weight from a vertice group, simply select the mesh and zero the weight settings for that group in F9. Then start coloring in the level you want.