After taking the frame of the car I could now take a better look at the holes in the back. These holes are the result of cutting the rear roof opening more to a square to get the width of the roof all the way down to the lower rear window lip. Through the holes you can look out of the car through the vents that are just above the rear decklid.
I really want to shut them, because they will let a lot of noise through. When driving the beetle I noticed I could hear the engine of the car behind me really good at stoplights. These holes is what causing it.
I decided to weld them shut with a piece of steel sheet.
My welding is not the best, but it is functional. Forming a piece of metal the way it would fit the hole was the most time consuming. after welding I painted it and then I put seam sealant on it and painted it again.
I treated the part on the inside, behind the air vents, with some anti-rust stuff normally used to protect cars from rusting.
I don’t think welding it is a must. Using some other form of noise supression material to stuff the hole, will be fine too.
The last two images show the sides of where the rear window used to be. You can still make out a slight curve inwards. This means, the hole in cut in the roof is just as wide as the rear window.