I'm rigging a model manually because I don't like Rigify. I forgot to enable X-Axis Mirror at the start, and clicking it now does nothing at all for some reason, so I did it the manual way that everyone reading this probably already knows (by default Numpad5, Numpad1, Shift+C, ., Shift+D, S, X, -1). This looks fine in edit mode, but when I go to object or pose mode the hand is twisted the wrong way, the arm IK works strangely, and the pole target (the sphere) is in the wrong place. As well as this, some bones are mispositioned slightly, but this is not a big problem. Anyone able to help?
UPDATE: Interestingly, when I parented the armature to the mesh with automatic weights, the mesh snapped into place exactly around the bones. Picture at the very bottom.
(Above) The entire armature as seen in edit mode.
(Above) The problems as seen in pose mode.
(Above) The mesh snapping into place when parented.