Angles will be the death of me

So I had to basically rework my project when I found out that everything had to be generalized for any skeleton that UPenn will upload to the database server. As a result, I rewrote everything so it would follow this; however, my 'hack' from the previous post to fix the angles no longer holds valid :( 


I tried figuring out angles using only Math.atan2 and failed. Then I tried to use rotation matrices, and I still failed. Now I am trying to figure out the math using quaternions. The results I am getting from using quaternions is so close to being correct. My program feels bad for me, it really WANTS to work, but it knows it can't flat out lie to me and work when it is not supposed to :( I really hope I can figure out what is wrong by the end of today...

It really wants to work...