I agree with all of that! Really wonder how a newer manual would help fuel economy. Be nice to have the gears in the housing but the advantage of an overdrive.
If time does not pass me by, I would love to find a crew cab of that era and do the Cummins swap. Given what new trucks cost, and the fact that I can live without all the bells and whistles, it seems like a no brainer. Update the drive line, but one of the best diesels, and the old Ford Crew cab body. If one could refrain from the urge to put 40's on it and roll coal, I would guess you would have a rig that could easily get upper 20's for MPG, or better, and do about all you would want minus hot shot work.
Time, money, sweat, tears, and box of curse words is all one needs.
Good luck on the project, and keep us updated.