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.

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.