I'm guessing all the bonename2 stuff happened when some bone heirarchy got dragged into or onto something else inadvertently.
I agree with Nancy that a startover would be in order.
There used to be a fine plugin for A:M called "the Setup Machine". After you put in the basic bones and weighted your CPs to them it would go thru and and add all the extra bones and do all the relationships and hide everything that you never wanted to see and give you back your character ready to animate. And it could do all sorts of multi-legged, multi-winged, multi-headed characters if you needed it to. Unfortunately it's discontinued.