Hi Steph,
Your Hashimotos could be the culprit here. I know there are a few members with Hashi's who will offer some advice too. Thyroid conditions can mimick lupus. Your anemia could definitely be part of the problem too.
Redrose gave you excellent information. Your ANA can change at the drop of a hat. It's not a reliable indicator of what's going on. Mine has gone from positive to negative and back and forth constantly. Don't rely on it at all to tell you what your body is doing.
I would make sure your thyroid is functioning properly, and definitely get started on that plaquenil. It can take up to 6 months to kick in. The sooner you're on it the better.
Good luck,
Ginny