The back of the trans itself will be about 10" behind the centerline of the wheels, which leaves plenty of room. You will need to cut / modify / remove the vert top storage though.
You will need to weld new linkage, offset a bit, but not impossible. Just run the bars toward the rear instead of toward the front. The actions of the shifter will be kept the same, you just need to route the linkage around the trans.
I'm playing with the idea of using a cheap junkyard cable shifter and making up some levers to form a quadrant box on the back of the trans. Seems like the easiest route at the moment.