Skeleton Re-targeting Problem For Same Skeleton

I exported the default UE4_Mannequin for use in blender. I imported it back in after modifying only the surfaces. I tried to re-target the original skeleton to the new(same) skeleton so I could get the animations to the modified version but odd things happened to at least 3 bones:

  1. the arm has been shifted out from both its socket and away from the hand
  2. 1 or both toes have been shifted down.