Your nickname on the tailgate will make the ladies giggle, but it'll be a good confidence check.

If you dropped the bed so that the upper rolled side bead was visually at about the top of the tire, then it would look better, and the proportions of the planned skirt to the bedside height would work better.

To get the door to work/look better the only thing I can think of is to drop the skin down with a light supporting framework behind it. That way you can leave the inner member (nothing to do with the tailgate) at bumper height and still have a more pleasing visual when the door is closed.