We do this all the time with open source drafting software, floor plans get converted to 3D models with ease, that's literally my clientele. I guess not many other people use that type of software so, it probably sounds more daunting than it really is.
I suggest that as you trace a line, you would have options for object type (like a wall), height, thickness, etc and just store that in the file data until later when it's time to import. This could also allow you to clean up your paper maps replacing pencil marks with clean vector image lines.