After the roof is removed you will have some ruff edges where the roof will lay. Carefully hammer and dolly the edges so that they are straight so that the new roof can seal tightly to them. Next grap a 3m Green grinding disc on a angle grinder and scuff up the edges that will be used for bonding. This is a MUST because the 3M Panel Bond (or whichever panel glue you are using) will need something to adhere to.
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Do the same to the replacement roof. Before you apply the glue, fit the roof to make sure that you have it where you want it, and that it fits. Secure it down, and walk around it and make sure everything looks ok. Make the areas in the front and the back were you are going to be spot welding the roof bare metal.