Plagues and other great diseases are important parts of history and some settings. They defy man and may even defy God in their swift and terrible punishment upon the body of society.
My issue with modifying/removing dwarves and elves is that the PC’s may want to play them.
One of the most powerful tools found in the World Building 102b article is the Worksheet. Here is a place to put the settings you might make with them.
A typical iron ore mine, the Irongate was closed some years ago and the entrance was closed off with a heavy gate of oak and thick iron bands, the Irongate. The mine itself was abandoned because it was a breeding ground for dire rats and many of the miners suffered from giant rodent bites as well as diseases from said bites. The mines are haunted by the ghosts of the men who died in dire rat swarms, adding to the mine's unpleasant character.