It took me a few days to find the solution.
Posting in case, someone else needs
https://docs.unrealengine.com/latest/INT/Engine/Animation/RetargetingDifferentSkeletons/index.html
Using my own custom character humaniod skeletal mesh/bone hierarchy from blender.fbx to create a clone animation sequence from AnimStarterPack (free in marketplace)
Using A pose (i think that’s what it is called)
Final result gave me a animation sequence, but with the mesh scrunched up into a ball
To fix it open, double click the newly created animation sequence
In the top Right hand side go to skeleton
LHS in Skeleton Tree tab, check Show Advanced Options
Right click “root” (should be the top bone)
click “Recursively set translation re targeting skeleton”
Should be fine now (All the drop menus should change to Skeleton)
The center point may have changed
Change Root and pelvis menu back to animations.