This has to be dealt very patiently. I want you to first put a tabular coloumn like this
M Tu W Th F S Su
Then record on the days she had fever. 6 weeks is a long time and you are giving several other important clues. 1. Skin rash
2. Head ache. 3 Marked reduction in activity.
Now let us divide the problems into infections and non infectious problems.
Infections like Malaria Typhoid your blood investigations should have revealed. As traveller you must also think of Rickettsial infections which respond only to doxycycline and azithromycin
Of course there is urinary tract infection
Child hood tuberculosis
is called Primary complex and will be revealed only by a Mantoux test
Then there are two important group of non infectious conditions.
A peripheral smear study is a must to see how her red and white blood cells appear.
ESR is a test which will give a clue about a type of Rheumatoid arthritis
which presents like your childs case : JIA.
There are other collagen
vasuclar disorder belonging to the family of Rheumatoid arthiritis which may demand specific blood tests.
Still if the answer is not found there are some more special investigations.
Usually, these problems end well. Patiently review with your pediatrician