The leak is above the roll bar at the seam. Is there anything I can use that will seal the seam but not ruin the top? Also same BS on the driver door but there's enough threads on that.

 

im assuming this is the top for your 07. You can go purchase canvas sealant and use it on the canvas. Clean it with 303 cleaner and then use a canvas sealant/conditioner. The tops on jeeps have to have maintenance done ever so often to prevent it from becoming brittle.