What could cause right flank pain, normal ua, nausea, low grade fever, inability to take deep breaths?

Flank pain: Suggests either urinary tract infxn (unlikely due to normal ua), kidney stone (don't always cause hematuria), musculoskeletal problem (muscle spasm; thoracic strain/sprain) or other kidney problem. May need imaging study to r/o stone. See fp for thorough exam, options for diagnosis & treatment.

Depends: Among the things that can cause the symptoms you describe are kidney stones (yes, many have a normal ua), collapsed lung, pleurisy, pulmonary embolism (blood clot to the lungs).