First off DO NOT go the soffseal route unless they have made some significant changes as their seals are stiffer (harder to compress). If one side only is raised up it would seem that side was not the same as the other before the seal was applied so there might be two issues, i.e. seal thickness and trunk lid fit up. As already mentioned the old faithful razor blade has been used more than once in this situation. I'd take the seal out and make sure the lid fits the same around the parameter and then put the seal back in and trim as needed.