I've been toiling with this for a while and thought I would throw it out to see what you (more experienced) guys had to say about it.
I own a 2001 bobbed Tacoma with a custom basket and wheel rack. Looks cool, but the functionality is pretty limited. The basket on the top is a bit of a wind catcher and the tire, well, lets just say I backed over a Corsica... and totaled it
There are a few additional problems I need to solve as well. My shocks just aren't doing it. I'm over extending them and bottoming them out... with OME springs. So I'm leaking fluid out my shocks and need to get some new ones under the truck after I solve this problem....
On a regular basis I take my M416 trailer out into the Rocky Mountains and camp and off-road (some of the off-roading includes rock crawling). I'm working twards doing some more expedition related stuff but this needs to be figured out then the trailer is another ball of wax. This is really about what makes the most sense from a storage and engineering standpoint.
So there are a few ideas, I just don't want to do this a second time.
Create a cage in the bed of the truck that allows for more shock travel and the ability to have a basket that moves from over the bed to over the roof of the cab (this is a daily driver right now). The tire would now be added to my rear bumper... Yeah I know it will still be in the way to a degree....
So another thought was to not cut through the bed and add shock hoops to the outside of the frame on the rear. I have enough backspacing to keep them from rubbing... I think. I can't seem to find the photo of this but I have seen it done.