There are half a dozen things that can cause pain in the urethra. Kidney stones are one of these things, however you did not have stones show up on ultrasound. That said, kidney stones in the early stage can be so fine as to be smaller than a grain of sand, and look like just a little grey sludge in your urine. It's bizarre to think they were looking for cancer, so throw that idea out.
There are other things completely unrelated to kidney stones that can cause urethral pain, such as a small skin tear or skin flap inside the urethra. These things happen for innocuous reasons like masturbating too hard, exerting yourself during exercise or sports, riding a bicycle, or no reason at all.
Microscopic amounts of blood aren't necessarily sinister, and may disappear as mysteriously as they appear, and also be related to a small tear or skin tag that gets torn when you urinate. What you don't want to see is visible blood or dried blood, but even then it may just be injury or temporary.
No one wants a catheter insertion. Intermittent and minor pain that lasts more than a couple weeks should be investigated, and yes, probably with that procedure.
For a wealth of information about kidney stones, check out the web site
http://www.urologystone.com where there are more than 3000 pages of information. Your questions about stones require answers far too lengthy to post here.
Beyond that, there are also such things as prostate stones, parasites, anxiety, nerve impingement, and other causes of urethral pain. Without your urologist's help, it may be exceptionally difficult to track down the cause, but expectedly none of the investigation what would be described as pleasant.
The STD swab you experienced previously is a dry cotton swab on a hard wooden stick, so of course it's not pleasant. Not saying that a cytoscopy is pleasant, it's not, but it's quite different. Hopefully you will be able to avoid it, but don't let your pain go unattended in the long hope it will just one day go away.