Mixed Connective Tissue Disease

I was diagnosed with MCTD in November 2011, one month before that I was diagnosed as Hypothyroid and was on Armour thyroid until March 2012. I've had trouble swallowing pills and right side of neck hurts—I had a fine needle biopsy on one thyroid nodule which turned out to be benign hyperplastic nodules. I dont know what happens next with these thyroid nodules. I also have Fibromyalgia and IBS diagnosed in 2006.
Right now I'm in some sort've flare up, I dont know if it's related to MCTD, Fibromyalgia or IBS. Or the gallbladder surgery I had a month ago. On memorial day I went to a outdoor picnic and stayed in the shade for 2 hours then went home, I had a very bad headache with sharp eye pains. The next day I woke up with achy joints and muscles, then had bad stomach pains with diarrhea—right after that these red dots appeared near all my joints, both wrist joints, elbow joints and ankle joints—-I've never had this happen before, the red dots got a little bigger and swelled up a little under the skin and now their round red bumps. I did go to the ER for the level 9 pain in my stomach and the terrible joint pains. Today I woke up and still had the achy joints and muscles and exhaustion. I took 2 tramadol for pain and that just take the edge off it. I get tired of going to the ER for severe pain and I thought having my gallbladder out would take care of it—and it was covered in adhesions. All tests for kidney, liver, heart was ok in the ER, dr there says if pains are related to MCTD I would have to see my reg. dr for more testing. I dont think my reg. Dr knows what to do, his clinic is the one who sent me to the ER the other day. I'm considering going to Mayo clinic in Rochester to see if they can help me figure out what I need to do to stop flare ups, or even control this MCTD from progressing. Does anyone else have Thyroid nodules or even these weird red spots near their joints too??