One thing I haven't seen mentioned (may be I missed it sorry) is the t-case output on a Chevy t-case vs. the Ford. All of the older Chevy 5 speeds were passenger side drop, IIRC. I believe the newer 5 form the 2000+ trucks drivers side drop, but pretty hard to find. Of course, that's probably a moot point, if you're going with an Atlas
I'd consider a 351W and a ZF trans from a mid-90's F-series. With a good tuneup my 96 Bronco I'd get 16-18 on the highway, even with the automagic trans. Those motors were all bullet proof 300 I6, 302, 351, 460, etc... hard to go wrong with one of them, IMO. Fuel injection wiring is a piece of cake, just get the harness and computer from the donor. You can also use your cable driven speedometer off of the t-case.
I'd go Cummins, if it were me, but I understand the reasons you don't want to. The Cummins motors are rattle traps, unless you get into a common rail.
My opinion... worth what you paid for it...