Unfortunately, most people in this forum seem to specialize in the North American, terrestial box turtles. With these species, intensive shell rot is uncommon. Some people do have the Asiatic aquatic box turtles, such as yourself, but they don't seem to be as active on this board.
If things are really that bad, I would suggest posting a message on the aquatic turtle forum. At the very least, shell rot is shell rot, and they should be able to give you some general advice. Furthermore, check around online. I wouldn't be surprised if there were over a dozen guides to raising malaysians and how to deal with their health problems.
Good luck!