The first thing I'd recommend is to research how the roof is constructed. Most of the videos I saw involve wood framing and plywood. Most, if not all, Winnebago MHs have roofs that are a foam sandwich with 1/8" luan plywood on each side of about three inches of foam and minimal framing. I don't know what they were like in '98 (my 2002 Class A is foam). If your's is a foam sandwich, most videos won't be of much help. If you have an overhead vent you can remove so you can see the edges of the cut out, you should be able to figure this out.
If you do have the foam sandwich roof, AZ Expert has some videos on repairing Winnebago roofs which should be informative. Here's one example:
Here's one involving a partially collapsed roof:
Even if your roof is a foam sandwich, there's no reason you can't rebuild the cabover part in a more traditional manner if that seems simpler. It's a fairly small area and hopefully the damage is localized. I'm assuming you want to keep your MH "until the wheels fall off" so you're not going to be too worried about it being perfectly restored to factory specs. Think of it as an upside down boat.
You can buy sheet filon (fiberglass) like that used originally:
Good luck and keep us posted.