Simple, really. You have to insert some vertices in your mesh, reposition them and cut new edges to follow the contour of the seam between the rudder and the vertical stabilizer. And, you'll also need to cap both of the resulting parts, so as not to leave open edges.
Actually, you should have set this up as you were "describing" the initial shape, so as to save yourself time. If you need more detail than this, and have Skype, PM me and I can show you how to fix this. Rest easy, it's not that hard to get what you want!
