I think vehicles that are this is tested on don't have a rear window that rolls down. With the rear window all the way down I think 4runners become more aerodynamic than other vehicles with the windows down.
I plan on making plywood panels in place of the plastic ones and cut out places for 6x9 speakers. You could add a piece of plywood to the back of the plastic panel to make it rigid and cut a hole to mount your 6.5 speaker. You would probably also want a grill or your speakers so they don't get...