I noticed you haven't had any response. So I am going to take a stab at it and say I would start inside to see just what is damaged. It sounds like you have looked outside on the roof already. Any insulation that got wet and is damaged will need to be replaced. As well as any wood roof ribs that may be damaged to the point that just drying them out won't do the job. There is a mildew issue you may also need to address.
Also, sometimes starting the work inside shows tracks to where the water in entering from if it's not obvious from the topside. The soft spots in the roof is not a good sign. But do not mistake the "soft spots" between the roof ribs on a metal roof as being soft spots. You just need to know where to step. My 1994 TT is that way. Don't know if your Newmar is constructed the same? The staining of the interior ceiling panels could be painted if not too bad. The orginal problem needs to be solved first before any finishing touches are applied inside.
Botttom line for me is the time elapsed since the leak began, the damage done over the years, any mildew issue needs to be taken care of, and roof structure needs to be addressed if damaged. Not to mention the repair of the point of entry of the water on the roof. Regardless of where it is.
Best of luck to you and keep us informed.