Clean out the area around where you cut. Make sure to vacuum or clean up any metal shavings that may have sprayed inside your roof, along your sealing, or on your interior. Next on any bare metal spray some etch prime, or some bare metal sealer to prevent it from rusting in the future or something along those lines.   
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You will need to fit the frame assembly back into the roof and drill the holes for the studs. You should drill each hole out with a 5/16” drill bit. Blow out the holes and clean the roof off once again. Once you have done that and your roof is prepped you can then decide what you are going to use to seal your roof. Street Beat provides a tube of silicon with the kit that you can use and is perfect for the job.   
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