Multiple symptoms still no answers

My son is 7 years old and has been having a lot of problems since birth but the last 2 years have been really hard on him.  I am going to list his symptoms here because the Rheumetologist is thinking Autoimmune just not sure.  We have had multiple tests run by 3 different Dr's nothing is showing a reason.  We are still waiting for results from a Periodic Fever testing because that takes longer to get results.  Only tests that was high so far was ANA.  

Fever comes and goes from around 99.8-102
Coughing that isn't helped by asthma meds
Chest pain (left side)
Leg pain, sometimes just mild but many days it affects his ability to walk as he can hold his own weight (which isn't much at 48 lbs).
Arm pain including hands and shoulders.
Neck pain, throat pain that comes and goes.
Swollen lymph nodes in neck comes and goes.
Abdominal pain usually lower.
Back back lower and around spinal area.
Eye pain, migraines, light sensitivity.
Nausea (throwing up a little).
Feet pain
Ankle pain
Muscles weaken after a few days of severe pain.
Jumping up and down seems to make a lot spots hurt to the point of taking all night to recover.  
Temp sensitivity (hard to find the right temp of bath water and can't stand to hot or to cold)
Allergic reactions to things still unknown but sometimes breaks out with hives can't always find the reason why
Dark Circles under eyes especially on the bad days

I think I have listed all the things we have noticed pretty much every day for the last 2 years.  He gets sick very easily and gets things like Strep throat easiliy.  Has had pneomia a couple of times in the last 2 years.  We have been in and out of Dr's offices.  He sees his Pediatrician, a GI dr and a rheumotologist plus goes to physical therapy once a week.  Has anyone elses child experienced this or known anyone that has?  He keeps missing school because there are so many days he simply can't move especially during the day and he cries at night from pain.  He is on Naproxen up to twice a day but that isn't helping the pain.  

[Dr. Kokil Mathur]

Hi!
I am sorry to hear about your son. In his cases all causes of generalized lymph node enlargement (generalized lymphadenopathy) and fever need to be ruled out one by one. Swollen lymph nodes across multiple areas or generalized lymphadenopathy can be due to viral infections such as mono or EBV or cytomegalovirus or due to bacterial infections like TB.  HIV or AIDS (contacted through contaminated needles or blood transfusions), leukemia, lymphomas and other cancers can also be a cause. This could also be due to inflammatory conditions such as rheumatoid arthritis.
Chronic sore throats can be allergic, viral or bacterial in origin. A prolonged illness in a seven year old can result in poor diet, anemia and fatigue and weakness. Many viral conditions like EBV (glandular fever) behave in this way with recurrent respiratory infections. With history of blood tests and hospital admissions infections peculiar to hospitals are common and are called nosocomial infections. Fungal infections in the body too can present similarly and need to be identified by scratch tests for fungus. A variety of drugs can cause drug fevers. Many cancers too cause recurrent respiratory infections.
Many parasitic infestations and worms increase the eosinophil counts in the blood and thus cause an increased risk of upper respiratory infections.
Recurrent or chronic fever is also seen in typhoid, tuberculosis, hepatitis, SLE, rheumatoid arthritis, Polyarteritis nodosa (PAN) and other auto immune disorders, UTI, sinusitis, otitis media, IBS, endocarditis, and parasitic infestations (like malaria), etc. It can even be diabetes and hyperthyroidism.
Please discuss all these possibilities with his treating doctor as a confirmed diagnosis is not possible on net. Take care!