In the top pic, I don't think it's shell rot. The pitting fortunately does not look deep. I'd do some gentle cleaning (use chlorhexidine aka Hibiclen or Betadine) and make sure that turtle can bask and the carapace AND plastron can dry off.
The Mississippi Map does have shell fungus on the carapace
The male RES has what I would think is a bacterial infection. Micropitting is a good description, and this usually goes away after one or two sheds. Fungus will linger unless treated.