I had a similar issue with my 1988 Jay Series 806. The previous owner had run some eye-bolts through the side of the roof (presumably to attach tie-downs) and through the years, water had worked it's way in. As the water damage was limited to several small 6" - 10" areas, I just cut away the rot, and pieced in new plywood. The plywood did not appear to have been glued in, at least on my model. There were screws from the underside of the bottom trim, as I recall.
Piecing in new wood was fussy work. If my canvass was off like yours, I probably would have replaced the entire panel rather than fussing around with fitting short pieces. It took delicate work with a chisel and Dremel tool. I used "wood hardener" around any suspicious wood left behind, then glued in good wood with construction adhesive. It's not factory perfect, but it's all hidden by the canvass. The important thing is to determine the source of leakage and fix it.
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