If you drill through the second layer and can't get it clogged, is it possible to make the outside hole slightly larger so you can slip in a patch that is slightly larger than the inner hole? I have heard that to get the foam out of the way you can use an allen wrench on a drill and insert the smaller end into the hole. Drilling it will reem out a small area to access second layer. On a side note, we use drill stops for carpentry that tighten onto a drill bit with a set screw. It works great for banisters and other detail work.
I'm about to do this repair to my boat, so I have been asking around. There are good ideas on this site
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