You should never rely on a forum for real medical advice, so you should definately follow up with a real doctor.
Do you have any pain anywhere else?
Kidney stones do hurt VERY badly and you might feel them pass as you urinate, but you probably would have felt even more severe pain as they moved through your bladder also.
I'm not sure if mine hurt as they passed or not because even before they got that far I had already hit an unbearable (for me) pain level and was on pain meds. I had a couple of large stones, but maybe if you had mutliple little ones it wouldn't be as severe until right before you passed them.