Negative results for lupus, rheumatoid arthritis, kidneys disease, thyroid disease, no protein in urine still having mild headache joint pain..etc?

Unrelated: If you have been taking Aleve (naproxen) regularly for a long time, you may need to be weaned off of it to get rid of your headaches. This is called conversion headaches. If the problem does no go away, consult a neurologist.

Arthritis: In some cases, the Lyme disease or tick-bone disease could give painful joints or even arthritis. Other causes are : Psoriasis, Gout, Pseudogout, some viral and infectious diseases.