I've been putting some thought into the expedition build on my 2001 F250 Crew Cab Short bed that I think would work for you, or at least give you some ideas.
I think you are on the right track by starting out lowering the truck and doing some mechanical work. Before you get into anything too big my advise would be to keep an eye on your oil consumption over a 3000 mile interval. Ford "officially" says consumption can be as high as 1 liter per 900 miles, but users consider this high. Solve any oil use problems, most likely culprits are the O rings on the high pressure oil system, O rings on the turbo, or O rings on the injectors. Once you have these issues resolved I'd start on the mods.
I am planning the following:
I'll start by linex-ing the bed , then installing an
AT FlipPac shell, internal storage on passenger side to hold stackable storage containers, top of storage unit forming work surface/extra bed, install
Heatsource heater, install
water tank and
shower system
On the exterior I'll be installing an
awning and a removable kitchen work surface and sink.
I'm trying to get all the work done in time for Overland Expo in April 2010