You seem to have many queries and perturbed. The most possible cause for your symptoms, as I see it, would be Calculi in the urinary tract
I am glad that your blood work is normal. Have you got your urine routine test done? If not, please do it. Also, get an x-ray of the KUB region done. This will rule out any urinary stones.
It is better for you to stop coffee consumption for some time until your symptoms subside.
Hope this helps you. Get well soon.