I did exactly what you are talking about doing. I used an expanding foam to fill the void. I used it because the repop piece was very thin and I wanted to make it stronger to block out without oil canning. Also, it seemed like it would dent very easily. As for the seams, I drilled the new panel along the lip and rosette welded it like the factory spot welds. I used dura-glass short strand fiberglass where the panel meets the sail area/ window lip. On the seams, I used body seam sealer. It seams very strong all around. I know it's not factory but it came out looking great.
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