I purchased an S3 from a RFF member, who goes by Dez. A beautiful body, but I still asked Don Goldberg to clean the finder (I'm a klutz when it comes to precision work). I got my camera back from him and have been happily shooting some HP5 with it and a 50mm f1.4.
Your experience and mine seem very similar: the finder is impressive but the focusing patch is not. I even think the Nikon S2 I used to have was less problematic, but that was some time ago and my memory may not be reliable enough. In any case, I think you did better with the S3. A lot of people sing the praises of the S2 (which is a really nice camera), but this one is better. I like the automatic exposure counter, the viewfinder, and the small indicator that tells you whether the shutter is cocked. I also enjoy the shutter speed dial (no longer divided in slow and fast speeds!!). See? The S3 is an improved S2.
Anyway, that's my story. And thanks for posting your photographs. They're really atmospheric and dramatic images.