Considering all the time and effort to make the quilt front, I would certainly re-position the sandwich layers and re-baste. Mark all the center positions on the top, sides, and bottom of all the layers. Line up the center marks. Baste the top half and then baste the bottom half.
I use a technique like this for putting all the layers together.
https://www.youtube.com/watch?v=jnke_KzeTI8