@brian14
I may have more to offer but first let me say I am not a medical professional nor alluding to diagnose what you are experiencing. As I said earlier, it does sound familiar. After suffering for many months I came upon a group of fellow suffers of BCG Adverse Events (BCG Cystitis, Reactive Arthritis, joint swelling, etc.) over on the Inspire.com website. One urologist who is often cited there is a doctor by the name of Michael O'Donnell of the University of Iowa. He wrote a paper titled "Infectious Complications of Intravesical BCG Immunotherapy". You may benefit from searching his name on the Inspire website and reading what his patients report. However, if you are like me you will want to download a copy of his paper from the website called "UpToDate". That website is a clearinghouse of clinical research papers. You would need to pay to subscribe in order to download it. I think it was $20 when I got it. Best $20 I ever spent though my doctors did not share my suspicion that I was suffering from a BCG adverse event. Many doctors do not think it is possible. Dr. O'Donnell states that it is very rare but does occur. I had to advocate strongly for myself to see an ID MD.
Also, the bacteria I tested positive for is devilishly difficult to detect. My Uro-Onco and PCP were extremely surprised that my ID doc found it. Many people on Inspire will attest that their ID docs made a presumptive diagnosis and treated them empirically based upon their symptoms because they believe there is a strong possibility of false negatives when isolating m. bovis.
Best wishes for good health.