HAHA. I would not call an NV4500 "clunky." The SM465 though, that is a different story, it is definitely a clunky transmission, but I love mine.
One more thing to consider, a 1992 Chevrolet C2500 with a 350 and a 5 speed manual (the NV4500) had an EPA mileage rating of 12 city and 17 highway. The C1500 was a bit better at 13/18 mpg city/highway. I would guess that one difference between the 1500 & the 2500 is rear end gear ratio.
https://www.fueleconomy.gov/feg/Find...on=sbs&id=9247
Sounds like the previous owner was headed this direction with the rear end swap. If you want to do any highway or freeway driving, or if you are interested in fuel mileage, you probably want to be 3.54:1 or higher, which means numerically lower (3.07:1 or 3.08:1)
My point is that the "old" drive trains aren't obsolete. If you build or buy a motor spec'd similarly to the 1992 Vortec (not the 1999 and up Vortec, that would be an LS) then theoretically you could achieve similar fuel mileage. Fuel injection should go a long way towards getting good gas mileage and having good driveability.
Assuming fuel mileage is a function of motor, transmission, rear end gearing, and aerodynamics, you could replicate many of these in the old truck.