You'll need to remove the rails and reseal them.
That involves loosening the A and B pillar trim at the top and accessing the bolts with a wrench (maybe 10mm??). You should be able to pull the headliner down enough to access the bolts without having to remove the headliner.
Bill Gill has a write-up in the Tech section regarding removal of the rails. It's for a D1, but the idea is the same.
Are you sure it's the factory rack and not a sunroof issue?