Itsmeb,
From the picture it appears that you're wanting the top to look like the old factory insert, but you've replaced all of the wood with metal. I don't know how you can mix the two approaches. My answer would be to weld in a metal insert formed to fit the roof or to use a suitable donor from a station wagon or perhaps a van and paint it body color. I don't see how you can replicate the original look after you weld in the insert, but others here may be able to give you some ideas about how to work the vinyl?? I don't see how you will ever get a piece of plywood to seal out moisture over the long term, and I think you'll be fighting rot & rust forever, just my opinion.