I have considered just using screws, but a screw into end grain on plywood is notoriously weak. I use deck screws to locate the stringers to bulkheads and occasionally I will strip one out in the ply. This is not loaded except for bending of the stringers.

Dan,
Don't you worry about the bow gunwale stringer rotating with just the single fastener? That position would be better strengthwise since you are not going into end grain.

I am also concerned about the screw hole being a starting point for water into the wood causing rot. Sometimes very quickly. You could always use varnish into the pilot hole before driving the screw, but it doesn't seem as good as epoxy. How good is good enough, of course.

Jeff,
It should be relatively simple to make a drill guide that locates off the side of the frame, for those with minimal skills. Actually after having angled a screw thru the side of a frame I was going to make one for myself.

I thought about using a furniture style arrangement. Drill a hole thru the stiffener, into the frame (approximately 1" deep). Then drill a circular hole (3/4" ??) thru the frame so the center of the stiffener hole and the new frame hole are in line. Then use a solid dowel as a "nut" in the frame hole. This would provide better pullout by having the side of the dowel pull on the plywood. The only thing is I wanted to have a smooth shank on the fastener where it would be in contact with the inboard / outboard hole in the plywood. Also I wanted a tight fit, and not having the screw threads cutting thru the hole (causing more opportunity for rot).
I could not find a screw to fit all my nit picking desires. Maybe I want too much.
Additionally the dowel would be very short and prone to cracking when you tighten up the screw. Possibly the dowel should be plastic not wood.
Another issue would be that the stringer would not have a very good "seat" against the ply, unless you slopped in some epoxy to widen the contact area.

Somebody improve this idea and let me know about it. Or let me know the obvious errors.

Marc