Good to hear from you, the pictures are good enough. I'm glad you found a shifter!
That indentation in the roof had a piece of trim in it. Since this car is a coupe it might be a little harder to find. Try NPD or 5.0 resto. Maybe there is someone on here knows or has some around.
Cleaning up the seams on the top is a matter of preference. Bondo is probably the easiest, or you can learn about leading car bodies. There might be someone in your area that knows what is involved. This gets back to your level of commitment, do you want to pull the glass? Anytime you add heat you have to be aware of what else is in the area. Ask around, there are people smarter than me that know how you do it. I know that is what you are doing here. If you don't get any answers here go on you-tube. I just went and looked on you-tube, there is about 34 million examples of how to do it. Watch enough that you see the commonality between them. That will help weed out the others. Again good luck!