This makes me think that the treads were sized correctly so that when they're finished, all the rise heights are the same. Make sure you check your local building code for proper rise/run requirements. There should also be acceptable values for overhang. Most treads that I've seen at the store have a little overhang built in. That way you install the treads, then risers, and everything falls into place. Disclaimer, I haven't actually done this project yet.