I had a similar experience with the strut bolts. I had owned the boat for about a year and had hauled her out at the marina where I worked, just to clean the bottom. The shop foreman wiggled the strut and said it was loose. We tightened up all the bolts (one was really loose) and sealed the nuts with 3M 5200. That was 5 years and 4,000 miles ago, and the strut is still tight and hasn't leaked. My boat at the time was 3 years old.
The other issue I had that was similar to yours was the loose stop cable. Actually, I had the steering cables themselves loosen also. I checked all the cable u-clamps in the steering system, and found them all loose. None of the lock nuts had been tightened up to the retaining nuts on the clamps. Something worth checking on any boat.
I haven't had any experience with the rudder flange, my bolts still look good. Good luck!