Your son was/is fighting a virus. Sometimes hives are a part of the virus. Sometimes it's a reaction to an antibiotic. Both have happened to me. My doctor said the same thing your son's doctor told you. Take benedryl.
It feels like you're still wanting a reason for these issues that are related but not necessarily caused by the same thing. One condition and treatment leads to another. I suggest the stomach pain is related to the diarrhea. However, you need to ask his doctor about it.
There often is not a reason for illness. He's sick. Doesn't matter if his symptoms are caused by one illness, 2 or 3. All that can be done with most illness is to treat the symptoms. You're doing that. He's been sick with one thing or another for several weeks. I suggest his body's resistance to illness is compromised which can lead to another illness.
As we said in your previous question, it is not uncommon for kids and even adults to be sick for several weeks, one thing after another. I missed so much time from my first professional job that my job was in jeopardy. In a few months, my body adjusted and I stopped being sick as often. I'm retired and am rarely sick even tho I spend time with my 3 yo and 5yo grandchildren who have frequent colds. My body, over time, has built up a resistance to most bacteria and viruses. My immunity is the result of my illnesses over the first half of my life. My body, unfortunately, has developed a resistance to a couple of antibiotics.
I suggest your anxiety and stress can lower your immunity. It's normal to be stressed.out when our children seem to be chronically ill. It's normal for children to pick up how parents feel, become anxious themselves. Both chronic anxiety and frustration can also lower immunity. Your children need to know that however unpleasant this is, they are OK. This is not serious. Their bodies will heal.
I suggest you focus on finding a way for you to take care of yourself. You need resilience to to manage your children's illnesses. You have been resilient. Your yesterday's post seemed to me to indicate you're wearing out, i would be worn our too. I don't know you so I can't suggest how you can feel less stress and worry. For me, I go for walks as well as change my thought from "I can't do this anymore" to "it is what it is and I'll get through it." I suggest if you stop questioning why and just treat the symptoms, yours and theirs, you will feel better. It is what it is. You can't change it. Face one day at a time.
Breathe, slowly. Air in through the nose, out through the mouth while thinking/visually.focusing on something relaxing. I see myself sitting on the beach watching the waves come in.