As for the IK handles, this might be a result of "double-transformation." No, I'm not sure exactly what that term means, but it has something to do with inputs nodes to your geometry. You might try (if you haven't already) deleting history on your model prior to rigging and then see you IK handles join properly.
I'm still focused modelling, so animation is an area I'm still trying to figure out myself, but I hope this helps.