Hi
Welcome to the MedHelp forum!
Most l;abs have a fever panel that looks into all the conditions that can cause recurrent fever. Recurrent or chronic fever is seen in tuberculosis (you say ruled out, but has he been tested?), SLE, rheumatoid arthritis, Polyarteritis nodosa (PAN) and other auto immune disorders, UTI, drug fever, sinusitis, glandular fever, otitis media, IBS, HIV, STDs, endocarditis, parasitic infestations, fungal infections, lymphomas and other cancers etc. Since he has painful urination complete urological examination by an urologist is a must. Also he should get a complete examination of heart and lungs. Hope this helps. Please let me know if there is any thing else and do keep me posted. Take care!
Regarding point 3- has he been tested with urine culture at those times for a urinary tract infection? Has he had an intravenous pyelogram during that time? Has he had a cystoscopy (provided no infection in urine found) to look for stones, evidence of interstitial cystitis, etc? Has he ever had his thyroid checked for thyroiditis during those times? See PM re: fever potential causes.