Wow, I don't really know the answer to your question. I suspect this is why no one else has said anything yet either.
I would suggest posting your question in the Auto-Immune community and the Rare Diseases community. It does sound like your son should have his blood tested for auto-immune. I don't know what the levels are supposed to be, but it does sound like this is going to have to be monitored throughout his entire lifetime.
There are a number of possible causes of rash and joint pain and the two you mentioned are among them, but I would expect them to test for juvenile RA while they are looking for causes. Are you seeing a rheumatologist?
The clinic that my son goes to seemed very confident in their diagnosis and wouldn't give a referral to a rheumatologist. I was hoping to glean insight from other sources to build my case.....
Check with your insurance company as some will let you go to a rheumy without a referral. At the very least the docs should understand that you want to get a second opinion. They may not like it, but it is your right.
My son was diagnosed with the same thing. He had severe joint pain, red speckles on his bottom, raised bruise like welts near his groin. I was told it was from his immune system attacking itself, and his kidneys and it would go away on its own. It eased up. But in the end, we found out my son is allergic to milk, and has a reaction 4 hours later. It comes in severe joint pain (triggers artheritis), and many other symptoms. Dairy also was to blame for his many ear and sinus infections, and colds. During his episode of HSP all his symptoms were more intense and painful to watch, he was only 2. Now all that GONE going Dairy Free!
I agree with txsilver. Follow your instinct and visit a rheumatologist anyway. Many of his symptoms seem like classic signs of juvenile rheumatoid arthritis onset - red, swollen joints with heat, fever, fatigue, rash, etc. It won't hurt anything to have him evaluated by a rheumie - even an allergist as mykids suggested. Maybe she's onto something as well!
The tough thing with kids that young is they don't have the vocabulary to articulate exactly where and how much they're hurting - other than the physical signs that are obvious.