You have had the 3 most used diagnostic tests for bladder cancer in CT scan, urine cytology and cystoscopy. Chances are pretty good it is all stones or those cysts you mention. For peace of mind if you have any doubt get a second opinion.
None of us are doctors so my hunch is what it is worth, not much. The cysts may bleed and are worth watching. Obviously stones can cause bleeding also among many other reasons. Long distance runners often have this problem. I even know 2 people that have passed blood in their urine of an on for several years with no known cause.
