Jake, I don't see how anyone here can say much given so little details.
It must be true that the symptoms are similar because Lupus is in the
differentials for Lyme
http://www.emedicine.com/med/topic1346.htm#section~differentials
There are six conditions on that "differentials" list that would normally
be seen by a rheumatologist. There's also "other problems to be considered
list.
There's a slightly different "differentials" list here
http://www.emedicine.com/ped/topic1331.htm
I don't know much about Lyme, but if the antibiotics haven't improved her,
in 4 years, and are ruining her liver, I'd say it's time to stop them and
see an expert.

Speaking of other problems, a lady who posted here for a while, told me
that an African who moved to Canada developed severe joint pain. As it
turned out, it was discovered that his body did not agree with our foods,
and once he bagan eating like he did back home, his symptoms resolved.
Another possible.

The diagnosis part (and other details) for Lupus are here
http://www.ghg.net/schwerpt/ASLFAQ/index.htm

I think a good start would be keeping a diary of signs and symptoms for a
month or so, then seeing a rheumatologist.
Best wishes in your search.
J [Disclaimrer I'm not a medical expert]

PS I think some here have mentioned that some rheumatologists are better
at diagnosing (or ruling things out) and some are better at treating. If
you want to post the largest city near her, maybe someone here can
recommend a rheumy. (no promises though)