talking from personal experiance i had a kidney infection, pain in kidneys (agony actually) my urine sample was clear but i ended up in hospital. i had no burning when weeing but had bad pain in my kidneys and it only showed in my bloods (i think cant remember much).
sorry cant be of much help but telling you what happened to me i wasnt pg though.
huni hope this has helped. my advice is go back to your gp and tell them you are still in pain.
take care rach xxx