Hi Flesh Forge,
Since this is an older post (and a long one) that has been resolved, please create a new post with step by step descriptions of how you are setting up your bind pose along screen shots of how you are setting up your bind pose as well as how you applying your animations to the newly retargeted skeleton.
Please also include what Version of UE4 you are working from in case there is a bug causing retargeting not to work as expected.
-Thanks,
.