444, this sounds like a non-specific viral infection, there are loads of them around at the moment (change of season innit...am just recovering myself)
Children react to them in very different ways than adults
They can say "tummyache" when they mean "headache", they can complain of "hurting all over" because they don't have the language skills to pinpoint it etc etc
The aches could be muscle aches due to the virus. Ditto the headaches.
If she is attending school, skipping around the garden, running around, has had a CXR, bloods, urine test, has no temperature and been seen by both hospital doctors and GP then she should be fine but may be picking up on your anxiety
Try to carry on as normal and see if she picks up your cue and continues to recover from this virus. Some of them can linger for ages (I am in my 3rd week of mine..) but really there is nothing more to be done than let them fizzle out by themselves.
Good luck, and hope she is 100% better very soon x