Seems about right. Apply all transforms to mesh and armature.
What you need to do now is to adapt the pose of your custom skeleton to match that of the epic Skeleton.
you need to go through, bone by bone, and copy the bone rotations from one rig to the other in Pose mode.
After the pose is set you need to apply the pose as the rest pose, and apply the armature modifier to the mesh.
You then add another armature modifier and hook it up to the rig again.
The final item you have is basically engine ready for retargeting.
Note that you arent shifting things to get the pivot to match. You are only changing rotations to the the exact same between the 2 skeletons.