A couple of things....
The gas 6.0 liter in the US first came out in 2004, I ordered one in fall of 2003 and waited a bit. All US NPRs are auto's last I heard.
The thought of avoiding the opaque roof seems a bit short sighted to me. There's ample framing up there to put in a plywood top and seal it appropriately, an issue you're likely to have anyway with a used box.
Many boxes have aluminum skins, I would certainly avoid them, very little protection and easily punctured.
State laws vary, but since RV insurance is much less spendy than commercial insurance, I'd sure like to see how difficult it is to register and license as an RV.
There are many opinions on super singles, but for a mostly highway truck, the duals will be fine. My go to answer, "Hey, it's paid for!" An added benefit is you can drive with one flat in the rear for a short distance with duals. You'll still need help changing tires unless you choose to carry special, and heavy equipment. And, lemme tell you, the shop tightens the lug nuts with an air impact wrench, caring little of torque specs. I have failed to loosen lug nuts standing on a six foot extension bar bouncing with just my scrawny self!
My first impression of my truck/8' x 14' box was, it's too big on the outside and too small on the inside. Of course, it's my big toolbox, and it is so easy to fill! I've driven it and parked it mostly in residential areas now since '03 in Los Angeles and environs. What I would think long and hard about is whether or not I could have a near flush to the cab size box, perhaps 7 feet. I parallel park most days, put the wheels as close to the curb as possible, and still over hang the curb a good bit. Also, I kinda over do the "close" part and have ruined a few sidewalls by rubbing up against the curb.
And yes, I have parked at Starbucks, backing into the normal spots, but typically against a block wall, I pick the most remote place to park.
Although the "rough ride" of a cabover is subjective, my goal from the get go was the shortest truck for the longest cargo space. That means cabover. I am inclined to think that "softer" tires may help, mine are at 90 to 110 pounds, and now ride smoothly. The biggest change in the years I've had it was new front tires and balancing beads. My local truck tire shop had some amazing stories of the help they've given their clients, and my experience is similar. You may know, but rarely are these truck tires balanced. I still don't worry about the back, but man, the front beads surely helped.
As to any front suspension changes, I'd certainly look into that, but it seems the best advice I've heard is to do all your building, and THEN go to the suspension shop with your weight clearly established. I would look for someone with more experience than your typical 4x4 shop and your typical truck shop. That may be a bit of a trick.
And, yes, I've thought a good bit of a conversion. The hardest part? I've a large folding lift gate that'd make a great back porch. I'd sure hate to lose it, but, man, the weight penalty. Sleeping back there on clear nights would simply be a dream.