As a Blender noob I too found the Hero skeleton a bit complicated for my needs. Based on what you did here I did the following…
I imported the UE4 mannequin into blender using auto bone placement option. This gives an almost correct skeleton. I then imported it again but left the bones as you did above. I then used the second set of bones to correctly position the first set. I put my mesh onto it using the pose method that you did.
When trying to parent the mesh to the skeleton it kept moving forward and turning 90 degrees, even though the location , scale and rotation were all reset. To fix this I exported the mesh as an fbx file and the re-imported it. This solved that problem.
Ignore the large IK bones - just hide them until you are ready to export it to FBX.
And so that others dont have to waste time making a skeleton I have attached it here. Note that once you export it to FBX you cannot re-import it - blender will break it again.
For the export set the Z axis to up and the Y axis to forward. I hope this helps 