kidney stones, may want to have an experienced surgeon check for hernias as well.
I'm not a doctor, so please keep that in mind, but I do feel your pain and can understand your confusion and concern.
Hematuria (blood in the urine) is usually an indication of a bladder infection, a urinary tract infection, or a kidney stone. You said they performed a CT and everything looked "clear", correct?
If the CT results were looked at by an untrained eye, a kidney stone could have been missed. Not all types of stones show up on film, and when they do, they appear as 'shadows' and can easily be mistaken for bowel gas. Have your results read by an actual urologist, not your PCP.
My particular type of stone (Cystine) don't show on x-rays, KUB's, IVP's, or CT's, but the trained eye of a nephrologist or urologist can catch them (they know what they're looking for).
As for your pain, do OTC med's help? If not, you may want to get hooked up with your urologist and have them prescribe some short acting med's, as it appears that your pain/discomfort is acute as opposed to chronic.
Good luck to you.