Hi Jimbo, for me there is no other alternative than to get out the mig welder and replace rust with good old sheet metal. If your not good with a welder well I guess you can always learn, my opinion is you can't make it much worse than bog or rust and you can always fix your errors if you make a mistake.
The roof is what I'd be more concerned about though, a sunroof is not easy to remove and replace with metal. Since the roof is so thin they tend to warn under the heat of a welder.
Best of luck with your project.