The gaff rig is a good rig for a cruiser in my opinion. Not superior to windward, but good enough. On a reach it is superior. I would not have gone to a bermuda rig on a Tiki21, but kept to Wharrams design. But surely there are Wharram e-groups that knows loads about this? What I would have asked myself is "how much do I beat to windward". Upwind is the only course the bermuda sloop rig is any better, and marginal at that.

Plywood not sealed properly will rot, fact of life unfortunately.

You want to build a new rudder? Edge glued pine.. How about proper Western Red Cedar edge glued with epoxy/thickened epoxy and glassed over? Rot resistant, light and strong.
How are you planning to shape the rudder? With a handplane, a router, a CNC router, beltsander or??
I have broken several plywood foils on old tornados. Even one rudder that was glassed with heavy tri-axial glass on both sides eventually broke when the glass sheared off the plywood. That was while we were experimenting with mega-rake on the mast.. I have never had a foil done with edge glued planks fail. I am sure one of those can break as well, especially if it is not done properly. But not yet.. *knock on wood*

Do you have any pictures of the foils and the rotted areas?