It doesn't sound like she's in dire straits, but how bad that is probable depends on the kind of winter we end up getting. It doesn't sound like emergency work is necessary, so I'd start with a few phone calls to your local roofing contractors and see what they say. Roofing is dangerous work in winter weather, so that is usually going to add to the cost IFF you try to get winter work done. I would see if there's a way to hold off until spring for the work, but NOT to choose the contractor - IF you're going to replace it, it's likely not too soon to call contractors: They are often booked up after spring arrives and then your choices become more limited.
From the description, it does sound like you need to have it reroofed, and probably also need to have the old roof stripped off first. Especially if you want the house to remain viable for more than say ten more years. I say that because you mention blackened rafters/plywood panels. Some of the underlayment likely needs replacing. Most roofing warranties aren't valid unless applied to solid, up to code surfaces. You DO want a good warranty, in my opinion.
It sounds like you're relatively handy, so it might be worth getting a couple of 25 x 50 foot tarps (or one if it's enough) at your local Home Depot and putting them down up there just to protect ceilings, etc. in the meantime. You'd have to make that decision - where is the water going that comes in? Anyway, use the tarps to direct the water to some harmless location and especially so it doesn't go down inside the walls.
I don't think there is anything you can do to make sure the matters don't get worse. The damage is probably already done; get a reliable roofer to check it out if you can't tell yourself.
About your present warranty: It may not be worthless. The contractor might be, but ... the manufacturer of the roofing material is likely still around and if it had a 3- yr installed warranty, that's still a chunk of change you might save. Can't hurt to research it a bit at least.
The black color by the way isn't necessarily mold; a roofer can tell you whether it is or not. It -might- just be weathered wood colors, but when it's wet and in the bad light as you probably had up there, it might have just looked like mold. Wood gets dark when it becomes spongy and the fibres are broken down. It didn't very likely get that way overnoght though, so you do probably have rot in those colored areas and other areas too.
hth,
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