We have a 2003 Kontiki too, but fortunately no evidence of your problems, is it possible to take some pics of the external appearance and that would help me learn what to look for (but hopefully not find).

Just thinking outside the box, would it be feasible to put a gel coat layer over the whole roof to seal any small cracks ? If it is leaking at the junction, then a wide cover + gel coat might be the best option to seal everything.

Welcome to MHF, must be said, it is good to discuss Kontiki things, our 615 was bought by us in 2006 and we LOVE ❤️ it. I have added Satellite TV, double leisure batteries, solar panels and numerous other little things (currently changing the adjoining and stopping the annoying 20 minute shut down).

So, please join in and swap ideas with us as you sort your problem - keep us updated.