How to fill these gaps between the body and the roof without cracking over time?
(Areas circled in the image below.)

And what is the best option to glue the roof to the body and that has a good structural union?

This image is merely illustrative, but we are making a well-structured ceiling with structural cores and carbon fiber.

I would use a methyl-methacrylate for the structural bond. 

For filling the gap, you need something with good flex to avoid cracking, so a polyurethane adhesive like Sikaflex wouldn't be a terrible choice. Do you need to fill the gap though? As long as it's nice and tight and uniform, a panel gap isn't aesthetically displeasing?

Methyl methacrylate was number 1 on my list of options for making the structural connection.

To fill in the gaps, we would like something that could do preparation and paint on the filling, so as not to look like it has been adapted.

Anything rigid enough to sand and paint is very likely going to crack over time. You can paint over flexible polyurethanes, but they are much more difficult to prepare in a way that will be invisible under paint, especially considering the shrinkage you will get. 

One option is to fill the gap with carbon fibre tow, which may be strong enough to resist cracking. Wont be easy to do neatly though, and I still feel you will get a good degree of shrinkage over time that will expose the join through the paint. 

If the roof is gutted underneath, you may be able to add layers of carbon tape over the join line to stiffen the join line up even further which would reduce the chance of cracking. if its metal, maybe weld it together with an overlapping plate, then slowly (to prevent distortion) weld in a thin metal sliver in the gaps to make a metal seamless join.  

Warren Penalver
Easy Composites / Carbon Mods - Technical Support Assistant