I also deal with rain rot and agree that is not what rain rot looks like; it looks like hives.
Ok, next set of 20 Questions
Grain: What kind of grain? How long has it been in whatever container it is in? How does it smell? Look?
How long since the container has been cleaned? What about bugs in the feed or in the container?
Annnnd last but not least, the run-in: Is it dry enough in there to where she can lay down if she wants to? My next thought is the possibility of:
1. Allergies to shavings or whatever bedding you might be using.
2. Spider bites but that is way out there because spider bites will generally "hive up" in a cluster, not scattered all over like what we are seeing.