A previous owner had drilled holes through the exterior skin and plugged with epoxy. This did nothing except place little stalagmites of epoxy throughout the cabin top.
THis is why I say re-coring the area properly makes far more sense than trying to drill and fill with thickened epoxy.
Before doing anything else, you have to figure out where the water that rotted the core came from and deal with that. You really do need to replace the entire core, because, the chances of core material drying out once saturated is almost zero.
I would recommend re-glassing, not re-using the pieces you've cut away. The reason for this is simple. The longer and more continuous the glass fibers in a laminate are, the stronger it will be.
I'd use end-grain balsa for the new core, as it is lighter than plywood, and doesn't have the disadvantages as a core material that plywood does. I'd also recommend tapering the core material and putting solid glass at any points you have deck hardware coming through the deck.
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You know what the first rule of sailing is? ...Love. You can learn all the math in the 'verse, but you take
a boat to the sea you don't love, she'll shake you off just as sure as the turning of the worlds. Love keeps
her going when she oughta fall down, tells you she's hurting 'fore she keens. Makes her a home.
—Cpt. Mal Reynolds, Serenity (edited)
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Still—DON'T READ THAT POST AGAIN.