Okay, I finally found a good reference photo:
http://www.rr-fallenflags.org/bn/bn2705ags.jpg
And here's what I can offer on modeling this unit from looking at it:
Start with Athearn's GP50, so you get the long fuel tank and the following parts:
º silencer from dynamic hatch
º Q-fans
º larger anticlimbers (although they look like they're the GP60 style - more square than rounded)
º flush pilots, so you don't have to grind the GP38-2 footboards off
Get yourself a late (corrugated radiator grille) Athearn GP38-2 shell and perform the following modifications. Remove the radiator fans and replace with Q-fans from the GP50. Make a vertical cut forward of the inertial hatch, a vertical cut between the blower housing and the first tall door and a vertical cut between the last tall door and first short door. Cut along the walkway surface removing everything from the first to the last cut.
Next take the GP50 shell and make a vertical cut between the last tall door and the first short door. Make a vertical cut between the second and third tall doors (counting from the short hood). Make a cut along the walkway surface to extract this portion from the shell. Place this section on the GP38-2 shell with the last tall door against the first short door. Place the inertial hatch/blower housing section from the GP38-2 shell against the front of the GP50 hood section now in place. Replace missing section between the rear of the electrical cabinet and front of the inertial hatch with sheet styrene.
Take a GP40-2 dynamic hatch (Athearn part no. 47201) and remove the exhaust (keeping the flared portion on the sides intact). Replace with the GP50 silencer/exhaust removed in the same manner from the GP50 dynamic hatch. Mark the amount of material to be removed forward of the radiator section to accomodate the modified GP40-2 hatch. Place the dynamic hatch in position on the body. Put some of Athearn's acetal handrails on the model and you're ready to paint. [Note: I use white, masking the ends and painting the rest to match the body color - Athearn part no. 46106 (GP38-2 handrails) for the sides and Athearn part no. 80524 (SD50 handrails - includes both early and late end styles) for the ends.]
Now you've got a reasonably close model of a late production GP39-2. There are certainly ways to do it with less work, but this just might be the fun
involved project you're looking for.