I'm having similar problem and wish someone would answer this. If there isn't a tool for this kind of operation, I hope it is something ESRI looks into developing. Sorry I couldn't help. I just wanted to let you know you are not alone.
you might want to look into Linear Referencing; Create Routes from your streams that have a direction based on a starting spatial orientation priority that overrides the digitized direction of the input features in the polyline segments.