Hello from JustAnswer.
Although you state your age, height, and weight, you do not mention your gender. I realize that you entered personal information when you registered for the site, but that information is not available to anyone reading these threads to assure privacy. I will include conditions from both genders, and you can obviously ignore any conditions that would not apply to you.
The pain and cramping does not help to identify the cause of the bleeding, because any cause of bleeding may cause pain or cramping. Most of the conditions can directly cause pain, but there can also be pain associated with small blood clots passing through the urinary tract.
Infection is one of the common cause of blood in the urine, but a urinary tract infection would no longer be a concern if the urine culture is negative and you have taken two courses of antibiotics. If male it is possible that there could be an infection of the prostate. There is no readily available culture method that will consistently grow the germ involved in prostate infections and antibiotics may not readily clear infections, so it is possible that there could still be a prostate infection.
It is still possible that there could be kidney stones. A CT scan will detect the majority of kidney stones, but it can miss smaller stones. It is also true that it could be a combination of infection and kidney stones. People with recurrent urine infections are at increased risk of kidney stones, and people with kidney stones are at increased risk of infection, and it is sometimes difficult to determine which came first.
Although infections and kidney stones are the most common causes of blood in the urine, there are a variety of less common causes, including inflammation of the urinary tract, vascular abnormalities, or growths within the urinary tract. Growths in the urinary tract can be benign or cancerous. The risk for cancers of the urinary tract increases with age and dramatically increases in smokers or former smokers. For example, bladder cancer would be the most common cancer in the urinary tract, and the average age of detection is at age 73 and 90% are found after age 55. So, at age 54, the risk is not a high risk yet, but it is a possible cause of recurrent blood in the urine.
You are correct that liver cysts would not cause blood in the urine.
If I can provide any additional information, please let me know.