Have you removed the roof rails? The bolts go straight through the roof so you need to bolt them back in and maybe dab some silicon around them.
Also, if the windscreen had been replaced by a previous owner maybe years ago, then the paintwork round the frame may have been damaged by the cheese wire they use to cut through the bonding and rust may may have began to form allowing water to get in. You can check whether the windscreen is original by checking the manufacturer marks on the glass.