Your message sounds very familiar to me. Waiting for a diagnosis is excruciating. Everyone on this board probably has a horror story about getting a diagnosis. It was a relief when my doctor FINALLY told me that I had Lupus (and MCTD.) It's better that being crazy and/or a hypocondriac.
Also, don't worry about the plaquenil. I gain weight extremely easily, and I never gained an ounce with the plaquenil and have never heard of anyone else gaining either. I actually lost weight the first couple of weeks (which of course I put right back on after my stomach got used to it!) The only side effect I have ever heard of is pretty rare - it CAN effect your vision. You should see an opthamologist at least every six months. If it did effect your vision, you would stop taking the drug and your eyes should return to normal.
After I started the Plaquenil, I actually STOPPED losing hair. But, I do think it may have lighted my hair a few shades. I don't count that as a side effect, but an improvement on my mousy locks! In my opinion, Plaquenil is the least intrusive of all Lupus drugs. Please read more about it if you can and try not to worry.
Anyways, your email interested me because I also have grain intolerences and PCOS! (I have a laypersons theory that someday they will draw a connection between PCOS and Lupus ... but that's another topic ..) Also, my Nana and sister are Celiacs. What kind of tests have they done for the gluten? Does your doctor see a connection between Celiac Disease and SLE?
I just finished reading: Living Well with Autoimmune Disease by Mary J. Shomon. I found it intersting because it connected the dots between my seemingly unrelated health issues. You might find it helpful.