EScanlon has some good ideas and direction. The paint flaking on your roof can stopped rather quickly (about 15-20 minutes). Flake off all the raised, loose portions of paint, then sand the edges smooth, but don't sand too much. Don't sand into the underlaying paint. Once you have sanded the edges, then take some clear nail polish (ask your wife/girlfriend/or just some woman at work) and paint the edges. This will help keep water from seeping under the edge of the paint and making it flake up more. (Note: this is only a temporary fix to allow you to focus on other things.) The issues with your hatch are directly related to rust, nothing else. The only thing to do for now is like EScanlon said, put some sort of treatment on it, inside and out, and focus on ther things. A complete swap of a good hatch is best, and a repair of the hatch will take quite some time. For now, treat it and leave it. As for the bubbles in your tar inside, I had some just like that on my floor boards. When I peeled it up, there wasn't any rust just clean shiney metal. The bumps were just from irregularities in the tar mat. The only way you'll know for sure is to peel it up. Get your self a heat gun or a halogen work light and place it close (but not too close, about 3") to the tar for about 1-2 minutes. Then take a putty knife and slide it under the tar mat. It should be pliable enough to just peel up. Then you can see how it looks underneath. Good luck on the project and have fun with the car.