Not taking folic acid
in first trimester can lead to what is called neural tube defect
in the baby,but not to worry now as if present should have been diagnosed in ultrasound by now.
Regarding large kidneys,there might be obstruction somewhere down in the urinary tract
which might have led to enlargement of the kidney,or other abnormality like polycystic kidney
might be a possibility,you need to go for a detailed anomaly scan,if no obvious anomaly detected then just go for ultrasound abdomen of baby after the baby is born,if any obvious anomaly detected discuss it out with your obstetrician and decide on what to do further.
Regarding prenatal vitamins
i don't think that there is any such rule of not prescribing them,intact we in INDIA recommend folic acid even before you have concieved.