Ground up type of deal eh?
For the electric fan question, I never had one on mine, but I did run my truck without any fan at all for most of this winter and probably will again. What I found is I had NO overheating problems at all, and for short trips in town, my MPGs gained 2-3 on average. Highway was something I wish I could have tested more, but didn't have much of that last winter with the slowdown in work. Best I could figure was a 1 MPG gain for freeway cruising. Most of the losses around town seem to be from the warmup time. Plugging the truck in might be an experiment for another day to see if that is indeed the case.
For the ultimate MPG IDI, I would consider 3.08s, but the difference from 3.55 might not be that big if you have an overdrive transmission. I'm at a loss to explain Towcat's experience with 3.07s though. I only notice a lag at the bottom end of 1st gear. Once moving I simply gear down and get the RPMs up as needed. For 70 MPH, 3rd gives me perfect hauling RPM.
I'm still not quite sure which engine would be better for pure MPGs though. The 6.9 has higher compression, but my understanding is the 7.3 has slightly better combustion chambers and a little more bottom end torque for twisting tall gearing.
You also need to consider what speed you will be spending most of your time in. If its all 70 MPH, then go as tall geared as possible. If its mostly city or urban, lower is better (4.10s are great around town).
I'd start off with a 2wd F250 regular cab and level the rear springs to lower the rear cross section of the truck. 5 speed manual would probably be the best bet for transmission, and a turbocharger might not be needed if the truck will spend most of its time empty. Just a good free flowing 3" exhaust. Stock sized highway ribbed tires at 80 PSI for all corners.
A truck like that could probably be around 5200lbs empty. A bed cover would probably help for highway miles and more than offset any losses in added weight.
If you are really thinking of going nuts with this as a MPG build, then consider a belly pan under the truck to smooth out the air flow on the highway.
I've also toyed with the idea of making a sheet metal plate cover to replace the grill on my truck. This would redirect the air flow around the front slightly. Not sure if doing this AND removing the fan would be safe, but for empty runs in the winter.....who knows.