Yea I thought you were tight on space back there. You could always go back to useing a cargo basket on the roof. I know you concern is the added wieght up high, however I would imagine on long expeditions you are prudent and drive more conservatively. You could also use it for carring the lighter items such as first aid, recovery(minus chain of course), nonrefrigerated foods, etc. A couple of storm/pelican cases and you would be set. for security you could permanently mount them to the basket by using some u bolts to fasten them to the rack. You would of course have to drill holes in the bottom but it would make sure your boxes wouldn't get ripped off. I know the pelican cases have a pad lock hole in them if you were leaving the truck in a marginal area.
I'm sure you have already contemplated this but I thought I would throw it back out to you. I would think that a wider cargo rack then you had previously would make a big difference in ease of use. The mega warrior basket from yakima is a perfect fit for the roof of a double cab. It is exactly the size of the roof.This makes for easy access by standing on the slider, since you do not have to reach way in. Just another thought.