One advantage of epoxy is that it doesn’t require strong clamping pressure. On the down side, the parts being glued, can slip around if the pressure is not even. Fastening the skeg is one of those situations where traditional clamps cannot be used. Using screws driven from the inside is one answer but it is difficult with the boat upside down and the molds in the way.
A simple method is to apply the regular epoxy adhesive to the joint but leaving bare spots near each end for dabs of 5-minute epoxy. Hold the skeg in place for 5 minutes by hand until the epoxy hardens. Once the boat is turned over screws can then be added.