That is what I would have thought (the spare space) - most of the 9000 ED discussions I've seen online are from 10+ years ago and have some outdated information. I can't be the only person still using the scanner and having trouble with Newton's rings.
I acquired my Coolscan 9000 two years ago and tried the following methods:
-Taping to AN glass ala
this article, but had issues if the film curved convex away from the glass.
-Using TWO pieces of AN glass, but theoretically adds texture since you're scanning through AN media
-Using AN glass above, and a 3D printed multi-frame mask (a different one for 6x6 and 645) below the film to press the film flat. Works, but cumbersome to line up.
I just mentioned in another thread that I bought the Media Sync/Stephen Scharf 3D printed scanner trays, and I'm super happy how easy it is to get individual frames flat (since it's clamped down on 4 sides) and clean (able to dust negatives directly as there's not glass sandwich).
Since you're already used to scanning frame by frame, I urge you to give his trays a whirl: