My rig is correct in edit mode and in the rest position state in pose mode. I applied all transformations (alt-g/r/s) to every bone in pose mode, but nothing changed. I looked in many forums for solutions, but could not find any. My rig was fine until I scaled down every bone in edit mode by 0.14, and deleted a problematic bone constraint. If appending is the best option, please let me know how also (Mesh has changed drastically since then).
Some constraints like Stretch To is depended on length of the bones. You can see, that constraint has Original Length property, that should contain the length of the bone. If you change scale in edit mode, the length property in constraint will not update, and this will cause problems in the rig.
Pressing X button near Original Length property will reset length to actual one.