Wow. That's a lot of rust! When you mentioned fixing "the holes" I assumed you were talking about making the repair directly to the vinyl top. That may be what MrSony was thinking as well. Regardless, it's good that you ripped that old water trap of a top off and found the real damage. (I always distrust vinyl tops.) A lot of guys have had to fix vinyl top rot on here. If they don't chime in, you can probably find some good threads about it. AFAIK, most guys patch the roof with sheetmetal, which is probably far better than fiberglass for structural integrity. I've never done it or even researched it, so I can't weigh-in.
Also, welcome to the sight! I'm only 5 years older than you and joined when I was 3 years younger than you, so I can relate!