1000 grit might be too fine as the clear going over it needs something to bite to. The clear will fill even large sanding marks so I'd go no finer than 220 or 400 at the most. The first PF I was in on making was the original Fathom PF and we used 80 grit!!! That was too course but even 220 grit marks disappear completely when hit with clear. Remember the more surface area you have the less chance you have of the clear pulling away from the insert down the road.
Be sure to get all the white sanding dust off the insert before applying clear.
Mike P.