I wanted to begin preparing some of the thoughts for your regarding your wife's symptoms and suggest information that may be useful for you to help her be evaulated efficiently and thoroughly. It seems that we have several areas in concern, so we'll approach them together in a step-by-step manner.
#1 Severe leg pain involving the sides and back of the thigh. You didn't mention which leg, but mentioned that she did have a past workup for clots in her leg but that result was negative. If she has any numbness or tingling, weakness, swelling (especially tight swelling of the calf), redness, tenderness in the calf muscle, I believe that additional workup is needed. If there are neurologic symptoms like numbness, tingling, or weakness, then she may have sciatic nerve impingement (pinched) or have a bulging disc or spinal nerve root impingement ... this would require further evaluation with a good Neurologic examination, and possibly lower back MRI and X-rays. If her symptoms are more leg, thigh, calf-type tenderness along with swelling, redness, or increased warmth, then I would once again be concerned about a possible clot and recommend she be re-evaluated using duplex Venous Ultrasound with check for augmentation, or the gold standard study, which is a venogram. A Venogram is a test where dye is injected into a low vein, such as in the foot, and the deep veins of the leg are viewed using X-rays to check for clotted deep veins.
#2 Pain in her right upper stomach area: This sounds like you mean that she is experiencing pain in her right upper abdomen, just below the right lower rib cage. Do I have this correct? If not, please let me know. This area is predominately muscle wall, and underneath it in the abdomen directly is the liver and gall bladder, if her gall bladder has never been removed. Again, a thorough physical examination along with some lab studies and a possible Liver and Gall Bladder ultrasound may be needed to view this region. I would also have the ultrsonographer look at her other abdominal organs while we are doing this study, including the liver blood vessels, kidneys, aorta, spleen, and pancreas if possible. Has she ever had gall stone disease? Physical examination and these studies would tell me most of what I would be concerned with in this region. If she has accompanying symptoms of pain after eating, nausea, vomiting, right upper abdominal pain radiating to her back or between her shoulder blades or radiating up to her shoulder ridge, then I am more concerned about the gall bladder and pancreas. Other possibilities include an ulcer or inflammation of the stomach or small intestine. These latter processes can be evaluated with upper endoscopy, using a flexible fibre-optic scope to look into the stomach and part of the small intestine.
#3 Joint pains. These again would need a good physical exam to see if the joint pains are inflammatory, degenerative, or possibly rheumatologic (like rheumatoid arthritis and related immune mediated arthrits conditions). Plain film X-rays may be of some help in this instance. If there is fluid built up in the joints, I would want to examine that fluid for crystals (*like gout or pseudogout), cells (type and number), culture for infection, and possible treat directly depending on the results.
#4 New bump on the upper right thyroid, headaches, neck flushing sensation: I am a bit focused on the bump here. It is essential that she be examined, completely and thoroughly from top to bottom. If a thyroid nodule is present, I would generally perform thyroid function studies like TSH, T3, T4, free T3 & T4, and obtain an ultrasound to characterise the nodule if I felt it present. If it's a cyst, I would either watch it or drain it and look at the cells under a microscope. If it's a solid nodule, a thyroid uptake study would be needed to see if the thyroid nodule is producing thyroid hormone or not. If it is, that is a bit reassuring to me. If it is not taking up iodine, that is concerning to me. She simply needs a competent and comprehensive examination.
If costs and bills are a concern for you, there may be a resource that can help:
http://ask.hrsa.gov/pc/ is an excellent resource for you to find free or affordable healthcare in your city or region.
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