from history its seem that he had CHRONIC RESPIRATORY DISEASE WITH SECONDARY GASTROINTESTINAL-GENITO URINARY DISEASE. your child may had fever and cough with sputum for 5-6 months suggestive of PERSISTENT OR PROLONGED COUGH which may have one of the following causes:pneumonia(bacterial,viral,fungal),bronchiectasis,anatomical airway defect,accidental foreign body ingestion,immunodefeciency disorders but we can not directly jump to conclusion.. history of recurrent infections ,associated symptoms ,past and current drug history need for further evaluation. if i had such type of patient i would advice for investigation like, complete blood count,ESR,MT(monteux test if any contact history of Tuberculosis patient),Chest X RAY,Sputum microscopy and culture for gram staining and AFB,USG thorax. on the basis of report i will decide to do either bronchoscopy,CT scan or Special investigation for Cystic fibrosis or immunodefeciency. i would start antibiotic short course like third generation cephalosporin and macrolide like azithromycin till i will get all my report. after that i would do further management. you have mention that your child is currently taking some drug.i would ask for drug history here as certain drug may cause red color urine like Chloroquine,Deferoxamine,Ibuprofen,Ironsorbitol,Metronidazole,Nitrofurantoin, Phenazopyridine,Phenolphthalein,Phenothiazines,Rifampin,Salicylates,Sulfasalazine. Another possibility for red color urine and stool suggestive of infections . i would advice for urine and stool microscopy and culture,stool for OBT and report for it. i hope you will satisfy with answer but with report and history,we will get the precise diagnosis.