It's been a while since I've posted here, but I'm still using my AeroLid to this very day, and it makes an unquestionable 10-15% difference on fuel economy. I agree with the others that you need to raise the profile of the rear of the shell. If you look at how I did it, I used a separate rear profile to raise the separation line above the origional tailgate line.
Good on you for using top quality materials too, the cover will last a long time if you do it right. I'm glad that I skinned mine in coroplast rather than plywood or building wrap plastic, it's stood up well in over a year and a half.
Here's pics of my build
http://ecomodder.com/forum/attachmen...1&d=1272764200
Hope this helps,
Swede