This would be an interesting job, and I think a guy with good skills could handle it. But I don't think it can be done without installing a new rubber roof.
I would begin just as if doing a new rubber roof. Pull the edging back around the entire perimeter. Pay attention to how they assembled the drip rails and sealant.
As for getting to the rafter ends, I don't think it is necessary to pull the entire sheathing off. Find each rafter and cut a window a few inches square out of the sheathing. How are the rafters attached to the wall caps? Probably just screwed, and that is failing again, maybe the rafters are splitting? Consider an alternative such as hurricane clamp style. Stimson might even make something that will work.
Then patch in the holes you cut. I always thought that if I had my rubber roof off (of just about any trailer) I would lay another layer of sheathing down, because the roofs are always barely adequate to begin with. Another 3/8" would feel great.
At that point, it's back to just being a rubber roof job. You could even hire out just that portion if you wanted, which really is the more critical aspect of the job. Or go with one of the membrane roof alternatives.