Finished weatherproofing the hatch/wing area. I did notice that the panel sits up an 1/8" higher than the glass but looks good matching up the emblem. Doesn't bother me in the least and only noticeable if you are nitpicking.
Here is the direction I went with the photos below.
For the Gas Filler Door I used toothpicks to make a gap between the body and that rubber piece that goes all the way around. Then I spread RTV to seal it. If that doesn't work then I will just cut off that rubber piece and caulk all the way around with the RTV Silicone.