Joe, One very common cause of a bubble is a problem with the body filler. When some people don't take enough time or simply don't understand filler they get air bubbles in the filler. In 1 to 5 years these air bubbles work to the surface and cause the paint to bubble. This is the most likely cause of the bubbles on the roof. The front edge of the hood could be this same problem too. The bubbles you have below the bottom edge of the window are the most likely to be rust through. In my opinion, the whole back half of your car and the hood needs to be painted. The cause of the bubbles needs to be found and until you do the sanding it's just about impossible to tell how bad it is. The good part is black is easy to match and your doors and fenders are good. Jim