Then, it was time for the Bondo. I put an initial base layer of filler over the affected areas. I sanded, then added a bit more where there were low spots. Sanded again, and then hit a couple of other obvious spots one time more.
Now, my approach to the roof was a little different than what other people would have done. Ideally, the whole front section would have been stripped down to metal and a larger area hit with a thin layer of Bondo, followed by a lot of sanding and smoothing and repeated process. However, my plan for the roof was different than a traditional smooth and paint to match job. I wanted to add a utility/off-road touch to the car by covering the roof with a tough, durable truck bed liner. Weird, I know. I haul mountain bikes a lot on the roof, and am constantly laying things on the roof, so I wanted to go this route. With the factory roof rack lines that were black and separated the roof from the rest of the car, I thought it might work. And, as a bonus, it would cover many of the small imperfections that would have taken hours and hours to work out. If not for the fact that I'm putting a bicycle carrier on the roof rack, I probably would not have gone this route. Hard to tell how it will look until the car is finished, with the complete rack setup installed.