Dave,
You are on the right track with your drilling approach. Drill smaller pilot holes to get your right angle alignment fixed. Once that is set, get some SS or glass tubing that the bolts can pass through and drill holes so you may insert the tubing in the rudder and epoxy the tubing place. That will isolate the rudder from water intrusion on the mounting hardware. You can grind the surface smooth once the epoxy cures and gelcoat over the ends.