I have frequently found that when the pain is at it's worst, other symptoms can be milder (fatigue, headache, etc.) and vice versa - as in the fatigue is practically disabling, but the pain, swelling, is milder. It's a confounding condition for sure. I know it's a full on flare when everything is acting up at once. My temperature fluctuates regularly also - especially in the late afternoon into evening, flare or no flare.
As for disability, you may be in a flare right now that is making your job seem less do-able. I'd give the Plaquenil time to take full effect. That takes anywhere from 3-6 mos. or even longer. For me, the biggest benefit was in the fatigue department, but also general pain. That said - if you really don't feel any better after 3 mos., I'd consult with your doctor (or sooner if things get worse).
Sorry you've struggled for so long without a diagnosis - but hopefully things will get better very soon!!