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.

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