Congratulations on the new Sport Coupe. Not sure if you plan on driving straight through or stopping for tonight. I'm sure you're excited and nervous. Good luck with your trip. I may have to stop by and see it on my way to Raleigh (Ncsu), have two kids in school there. Id love to look at it and compare it to the one I have that needs restored.
I've seen cars with the paint damaged by trash bags used to either cover a broken window or just left laying on the paint for whatever reason. These were dark in color so the clear may not be an issue at all. It may be the heat absorbed in the dark bags that does the damage. I wouldn't think it would hurt the top material at all anyway.
Good luck and post lots of photos, inside and out.