Hmmm... well, there’s a lot going on there, not sure if they’re all related or not. I would say some of the genital area issues sound like Prostatitis to me. I’ve had it before, and symptoms can be itching/burning when urinating, some burning or discomfort after ejaculation, and general discomfort in the testicles & perineum, which can make it very uncomfortable to sit. Even the entire groin area can become uncomfortable. Sometimes Prostatitis can affect your overall feeling as well, like having a fever & feeling flu-ish or run-down & possibly even some stomach issues.
It could be that you just happen to have more than one thing going on - in addition to Prostatitis (if that’s indeed what it is), you could have a low-grade virus, maybe brought on by a weakened immune system from the other issue.
Obviously, the #1 bit of advice most ppl would give is to see your reg Dr. He or she would want to check your prostate, prbly run some blood & urine tests, etc. Even tho you already had a urinalysis, they may not have been looking for certain specific organisms that could cause these symptoms, so it’s worth getting tested again. I’m sure blood tests & other exam findings could indicate whether you have a separate issue related to cough, etc. Coughing up blood is a little concerning - definitely see your Dr.
Please check back in later & let us know what’s found - we can all learn from your experience....