Wire brushed (aggressively) and treated with Bilt & Hamper Hydrate-80.



I also thinned it and loaded the Hydrate-80 (20% water, it is water based anyway) into the inner edge so it penetrated by capillary action under the tray/glass covering areas that I could not reach with a brush, after an hour I used light air pressure and tilting the glass onto its edges to force it into any areas that might not have received coverage due to air-traps.
Left to dry overnight them I attacked it aggressively again with a wire bush and re-coated with Hydrate-80. Whilst this was drying all rust flakes were removed from the seal (surprised how much was in there) and this was blown out/brush clear.
Black Primer and two top coats of Satin-Black.

The next step is to prepare/clean/oil the cassette, then apply PU Adhesive to the seal and whilst that is still soft attach the glass/frame to the runners and close the roof slowly to the closed position. I hope excess PU Adhesive will "fill the voids" left after the rust was removed.
Once set I will use a fine tube nozzle to seal the top seal edge and "in-fill" the inner edge to prevent moisture ingress.