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.

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.