Bob,
The balsa core is a consistent thickness throughout -- except at the edges, i.e. near the caprail. I agree with the use of unthickened epoxy as the first step; it tends to run into the spaces where the deck may have delaminated (delam can exist even if the core is dry -- these are production boats).
Epoxy thickened with filler is great for sealing off the repair and when smeared into an undercut in the seam you've cut, strengthens the joint. Coring material (marine plywood, airex, balsa) weighs less, is less expensive, and is easier to install than a glass mat build up in my strictly amateur opinion.
--Dave