I actually figured out a decent method for using png sequences in an fbx. By assigning each image to a plane, showing each plane for around 5 frames, then moving the frames dramatically off screen (-50000Y) I achieve a decent transparent animation.
I will admit that I have the benefit of using some pretty beefy hardware with this method.
note: do not leave things at zero on the z axis, took me a whole day to figure that out.