Hi,
I just tried to extrude just a simple “window” with a clean mesh… but still have the same problems like with the unclean mesh… i even packed the window UVs the same way you did but i still got black spots and issues in UE4.
And i’m using a 512 lighting map… which should be a way to big for a a simple window…
this is just the window mesh, if you have time maybe you can take another look on it,