Since I started this thread so very long ago, I thought I would weigh in. In a way, I was "pleased" to see that cavitation is the likely cause of the pitting on the rudder. It was my working hypothesis when I saw this on our R-27. But I could find nothing on the prop that I would blame for excessive cavitation. I did the same procedure of cleaning everything up with sand paper and a dremel tool to catch any nicks or irregularities. But I never ruled out one other possible source for the problem. I kept my 27 in a hot marina that burned through prop anodes pretty fast, even with a galvanic isolator on the boat. What was so striking about the anodes is that they did not erode evenly. I often had "horns" develop on them due to irregular wear. Just the kind of shape that at high RPM's (I cruised at 3600) would throw bubbles that would then pop on the rudder, causing cavitation.
I never ruled this potential cause out, but if you notice your latest post, you have "horns" on the eroded anode in your before picture.
I can think of lots of reasons this is probably wrong: (1) flow separation around the shaft area of the prop puts the anode in a relatively low velocity location, making it less likely to throw cavitation bubbles and (2) the erosion of the rudder is more in line with bubbles being generated at the tip of the prop blades). Still, worth some idle speculation.
Good luck with your fix. BTW, I have not seen any indication of this problem on my R-29CB and was looking for it right away.