so your animation doesn't face the right way
and when you rotate the top bone in the hierarchy it messes things up.
Solution:
add a root bone, follow this tutorial https://www.youtube.com/watch?v=a3rdumN9WUA and then export using game exporter for maya, it doesn't matter in the animation or if the mesh comes out with no animation, what matters is that he's got a new skeleton with a root bone.
we'll be re-targeting the animation from the original ninja on the new.
first you should open your skeleton asset in UE4, click re-target manager to open the window with all the red line, first select your rig for humanoid, match all bones to the one in the ninja, then click save and put the data anywhere in the content folder, preferably with the skeleton, then open the new one with the new root bone and load the previous data this time fill in the Root bone.
this is how mine came out after exporting, no doubt i did something wrong for the animation not come out, but eh we have a root.
just rotate him and repeat the steps but with a root bone inputted, with both you want them both in a T pose and click modify pose at the bottom, then click current pose.
you can now click any animation owned by the ninja skeleton, and retarget it with a root bone added, this is very useful to me for all the idle animations.
now I've found doing this to an animation that moves forward and backwards like a running/ sneaking, without an animation inside the root you can not lock the root in its place so you need to copy paste the movement from the hip bone into the root so it can lock it.
It still comes out strange because of the export but now that you have the forward movement you can lock it.