Very nice James, will be looking good for this season
When I looked into getting the Nismo sides, Phil said they were no lower than stock, so you should be fine with clearance on them. As for the line, I think it would look good with it deleted, or maybe paint below the line black and above it colour matched to the car, I've seen that before and it looks good. But smoothed would definately look good.
Still not sure on clearcoating the roof. I think it would be a lot of effort to get it deep enough to flat back to give a glass like finish. Maybe get the shop to try it on a small piece if you can get hold of some to see how much effort it is and if it will even work.