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Thank you to those who responded for your suggestions, guesses, & prayers. My 4-yr old celiac son's neurologist appointment is Nov 22. His pediatrician was right -- "you know how the best restaurants at the beach always have the longest lines, well that's how it is getting into the offices of the best neurologists in Charlotte". Yesterday my son had very little pain, but the day before, he screamed & cried about his thumbs for 25 minutes. Poor little guy. Today, no pain so far. Knock on wood that it will continue! For the many who inquired, my kids never play video games & very rarely play computer games, although they do like to build with Duplos & Mega Blox. Also, their diets are not stellar, but they do eat from all food groups each day & I give them a daily multivitamin. Here are some excerpts from what you guys had to say:

1. Watch him as he sleeps. Does he sleep with his hands in little fists with his thumbs tucked inside? That's what I've discovered about myself, & I do have intermittent thumb pain.
2. I was diagnosed with Celiac 10 years ago, & I've had thumb pain a lot. It's not at the tops of my thumbs though, only in the joint that connects my thumbs to my hands & usually both thumbs at the same time. Usually an ache that can be very painful at times & doesn't last long. I never really thought anything weird about it until I read your email. Taking a couple of advil usually works for me.
3.The only thing I can think of is possibly sending him to a doctor who practices alternative medicine, if you are open to that.
4. I was celiac as a child but was not dxed until my 40s (& very ill all my life, I might add). I had terrible bone pain as a child & the doctor always wrote it off to "growing pains". However, it persisted into adulthood. When the doctor put me on DHEA later in life, it helped enormously & when I went sugar & gluten free, it totally went away. Now that I am gf, I notice that when I get a little gluten or sugar (another intolerance), I get finger pain & joint pain in general--not necessarily in all joints at the same time, tho. Alot of the time, it is in just my thumbs &/or fingers. I am a pianist & love computer games, incidently. Your son wouldn't be into computer games that use his thumbs, would he? Just curious. My son used to have finger pain at around your son's age (5-6) & we wrote it off to computer games. Have the doctors thought about checking calcium levels or ferritin + iron? I know it is not uncommon for children to have deficiencies, esp when they have been untreated celiacs for awhile. I was severely anemic as a child & so was my son. I also had osteopenia. I don't know how long your son has been gf. I have noticed that I still get very bad leg pains prior to dinner and before bed. I noticed that taking my vitamins actually makes the pains go away. I think I may still not be getting enough nutrition. 
5. Just a guess, but could be peripheral neuropathy, which is pain in the nerve endings. The pain can be anywhere. I get it in my toes and legs. In addition to celiac, I have a rare liver condition, called porphyria, which causes among many other things, low blood 
sugar. I have to work very hard in keeping my blood sugar up to normal levels (yes, I test daily). Peripheral neuropathy is also 
seen in diabetes (blood sugar changes) and in cases of malnutrition, which celiac causes prior to diagnoses. What helps is B vitamins, or if sensitive to that, then adding foods that are rich in B vitamins, like dairy products and even pork.
6. PLEASE don't wait until his pain becomes unbearable to give him ibuprofen! The way that stuff works best is by giving it continually. What's the point in making him suffer? (I clarified to this person that I did give him some ibuprofen before bedtime one night when he was having thumb pain, but I'm just trying not to do the every 6 hour plan and have him be drugged 24/7.)
7. I was getting all kinds of bone pains, usually in my toes though. I increased the amount of calcium I was getting, also started
probiotics. Does he get yogurt? For some reason yogurt helps in this department (also helps prevent arthritis ... it was in an
August issue of Science News). Vitamin K might help too (it's in green vegies, also it's produced in the gut, but if he's been on antibiotics he might not be producing any ... it has to do with bone growth and connective tissue). Vitamin D is important too, and some kids don't get enough esp. if they don't go outdoors much or wear sunscreen a lot.
8. I get odd mysterious pains, mostly in my low back and legs, when my gut is unhappy (they are a first sign usually). Extra calcium/magnesium/zinc, and B vitamins seem to help, and Pepto Bismol is some sort of wonder healer. It is very peculiar - sometimes out of the blue it will literally feel as though someone has thrown boiling water on my legs, or a nail is sticking in my heel - this stuff really does hurt, though I think it is either referred pain or just crossed wires of some sort. I don't know much about acupressure, but do believe in the meridians of Chinese medicine, and wonder if you might find some information in that direction (rubbing his feet might help - seems there are nerve endings for every organ/part of the body that end up on the soles of the feet).
9. How about intermitent severe finger pain ? It rarely happens, but when it does there seems to be no reason for it - no
swelling or redness. The it goes away as suddenly as it started...
10. I am a grandmother & always got pains in the ends of my fingers (but not the thumb!) whenever I ate black pepper. So maybe look for a food reaction. Hey, it happens - doctors will look at you funny - but they do not know everything! Make a journal of what he eats - & beware of those little things - it could be happening as soon as an hour or so, or sooner if food. Just notice what he eats one day & see if he has any pain - it is like being a detective - of course it could be anything else also. Check acid foods? like tomatoes, citrus, etc - if he is drinking orange juice - switch to 100% grape juice - I find grape juice very soothing to my insides.
11. If you mean, by top, the joint.... try eliminating tomato particularly tomato sauce and see if that helps.
12. Can you relate the pain to some activity? A game or toy he plays with? I'm not familiar with the nerves in the upper (dorsal) part of the thumb. But they all feed through the wrist. Try massaging the wrist rather than the thumb. You can also try wrapping the wrist with warm moist wash cloths. If it's happening on both hands at the same time I'd ask the Dr to look at his neck & upper spine. The nerves that feed the arms & hands come out somewhere in there. I'd also look at the way he's sitting before the pain begins. I can understand you not wanting to give meds unless they're really needed. I'd try all the non-drug things and if they don't work within 30 min I'd medicate... maybe with 1/2 the dose. It's easier to control the pain if you medicate early. Breaks the "pain cycle".
13. Does your son play on the computer or the television games? Does he hold a computer mouse or play station devices? Overuse can promote hand / thumb pain related to carpal tunnel or just overuse. I have extreme right thumb joint pain and have had off and for a few years. But, I also have back, hip, and pain that radiates into the legs. I did confirm I have a back problem that causes the pain in the back and legs, but there is no explaination for the hip and other joint pain. I have had every antiinflammatory / arthritic / rheumatoid test there is and all were negative. I now think the hip pain is solely related to celiac. The thumb pain to celiac and /or overuse. I have to limit the use of my hand at times and "resting" the joint does seem to help. It is my understanding that one of the effects of celiac is joint pain.
14. As a physical therapist, here are a few things I'd rule out: 
-nerve impingement in the neck or upper arm, or other nerve damage
-peripheral neuropathy -the type assoc. w/ diabetes
-Guillam-Barre syndrome
-thyroid dysfunction
-check activities during the day - is he using his thumbs for a game or other acitivity in an unusual way, or check how he positions himself while sleeping
-arthritis
I doubt it is any of the first 3 issues, as they typically don't exhibit the exact same symptoms on both sides of the body simultaneously. I merely listed those to rule them out - most likely it is an unusual activity that no one has observed yet, or just some odd growing pains.
15. Maybe he had some nerve damage while undiagnosed and the nerves are re-growing now...which is really painful (I had Bell's Palsey and remember the return of my nerves). I know that if I ingest gluten I get all sorts of weird pain - sudden and sharp in the ends of my toes last night and in my hip joints. So, maybe prior to diagnosis he had damage? Might take him to a chiro or messeuse? I've taken my 6 year old to a chiro (they use a break-away table rather than the old twist and pop method - yuck) and she really benefitted from that. Possibly a homeopathic remedy for nerve pain could help...Hypericum Perforatum, specifically, might be helpful...I've given my kids homeopathics over the years with pretty good results. Best of all, its so benign that you don't have to worry about giving it to a child several times a day for a couple days, unlike keeping a kid on Ibuprophen all the time...that can get worrisome.
16. I talked to the ped and rheumatologist today as my 18 year old daughter who is away at college can't sleep due to sharp pains in her big toe and middle finger...she has a variety of health probs along with the CD & also has a neurologist but no one can explain it.
17. The Dr should have xrayed his thumbs -- maybe it's arthritis setting in.
18. Since people with Celiac are more likely than others to have more than one auto-immune disorder it could be Rheumatoid Arthritis. It would be worth looking into. Auto-immune disorders are so illusive in the pediatric stages so it may be presenting itself as just joint pain in the thumbs.
19. This sounds to me like a nerve pinching in his upper back, neck or even upper jaw and shooting down to his thumb tips. I get pain in my hips from clenching my lower jaw. While waiting for the good neuro to see you, maybe you could take him to a myofacial or reiki therapist. They have a better understanding of the soft tissue/ nerve connection and heal without surgery. Neuro's are usually trained in surgery and love to perform!
20. Our very gluten sensitive daughter, now 23, had excruciating pains in her knees and legs as a preschooler and school age child. I don't remember pain in her hands although I'll ask her. After much testing (not gluten testing back then), the dr called them "growing pains", which meant, "who knows". I believe joint type pain is connected to gluten intolerance.
21. I have arthritis and sometimes my thumbs, among other places of course, just hurt really badly. I know there is a connection to celiac/arthritis, but I don't know about juvenile arthritis/celiac connection. I make a rice bag for my aches that helps. You could take a cotton sock, put some long grain rice in it and heat in the microwave for about a minute, time varies, and let him hold it on his thumb when it hurts. Remember to test this as it can get really hot, may need to wrap in a towel for him.

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