I don't have the exact same diagnoses, but I have Sjogren's, hypothyroidism (not specifically Hashimoto's) and undifferentiated connective tissue disease, which carries many of the same symptoms as Lupus. I am taking Naproxyn, Plaquenil, Evoxac, Amytriptilene (for sleep issues), Baclofen and Tramadol. I was having lots of bone, joint and muscle pain, in addition I have foot pain, gastritis, hiatal hernia, heel pain, peripheral neuropathy, dry mouth, localized muscle atrophy and so on. After fighting doctors for 5+ years, I finally got a decent rheumy who got my meds lined out and I am doing pretty well. I still have foot pain (mostly heel pain) and the peripheral neuropathy, but most of the joint, muscle and bone pain is gone (at least for now).
Fatigue and sleep disorders are very common among auto-immune patients from what I gather. Good luck to you. If the doctors you are seeing aren't giving you enough info you have to make them. Take a notepad with you with all the questions you want answered. If your dr. doesn't want to answer your questions, get another doctor.
Oh my, you certainly have a lot to deal with. I don't have the same but did have ulcerative colitis (until total colectomy and J-Pouch), hypothyroidism and just lately Lupus. Yes, the exhaustian can be awful. I've seen some improvements with the Plaquenil, reducing stress and taking supplements such as fish oil capsules, good vitamins, selenium, CoQ10 and vitamin D. Am now getting neruopathic involvement and abdominal wall pain. Just started depression meds to deal with this plus other life events and am trying to appreciate the things I can do and trying not to think of what I can't.