Mike - I just did a similar repair in the inside bottom of my canoe. I guess I hit a stump, because there was no visible damage on the outside, but inside the glass and wood had cracked. I could feel the sharp edge of the glass at the edge of the crack, and when I leaned on the gunwales, it would spread open a whisker. To repair it, I random orbit sanded down to the epoxy, completely removing the varnish. I then layed a cloth patch over the crack, going well beyond the visible crack area. Then I soaked the cloth with resin, and finished up with a couple more coats to fill the weave. During wet out, I flexed the gunwales again to work the epoxy into the crack. After a final cure of about a week, I sanded the area, and it is now ready for varnish. Since I plan to do the whole boat anyway, it will get varnished when I get to it.

Hope this helps. - John