Well as I see a few problems with this kind of build.
1. With the door opening and closing all the time your really going to have to reinforce the whole pannel becuase of the wieght. Think a 5 lb weight on the door suddenly stopping when the door stops.
2. Resonances. With all of the pressure that the sub is going to producing its going to be hard to keep everything from vibrating and sounding like crap.
3. You have the mid and sub in the same airspace. This means that the sub output is going to effecting the mid driver probably making it sound not very good.
4. As already mentioned clearance issues.

This does not seem like a project to be taken lightly. Its going to take a lot of time and skill to pull it off correctly. Not saying it cant be done but being done and done well are two seperate things. Imo youd be better off putting the sub "freeair" or infinate baffel on the back shelf like how a lot of cars have 6x9's, and sealing the trunk off.