There is no way to get quality bass out of the stock location, short of possibly filling in the tailgate with fiberglass to seal and silence it. Even then, you would have rattles. I believe the direction I am going is to use the stock subwoofer location for a midbass driver much the same it is today. However, I will check to see if a can get a shallow mount woofer in there. I'll likely build a custom crossover so that this woofer only sees 70hz to its natural cut-off
I then plan to take a feed from the speaker level outputs (unless I have find line out pin outs) and use a CleanSweep, Rockford, or Alpine factory sound system integration unit. I will then feed a stout amp, and a custom subwoofer enclosure. The enclosure and amp will be connected with quick disconnects so the whole unit can be easily moved in and out. At this point I am thinking of four 10" woofers in a flat on the floor sealed box about six inches high.
I am also entertaining a much simpler set up. . . An Alpine LAT sub which uses six 7" woofers in a lateral array. It is a small enclosure and has a built in Alpine PDX amp.