The 2300 hp rated GP39 had a V-12 turbo engine, while the 3000 hp rated GP40 had a V-16 turbo engine (the 2000 hp rated GP38 had a V16 non-turbo).
The GP39 had a turbo exhaust stack like the GP40, but only 2 radiator fans and shorter radiator screens like the GP38.
There was what was called a "Phase III" GP39-2, which had the engine and DB shifted rearward some 3 feet (along with the corresponding doors) for better weight distribution. If I am not mistaken, all of Santa Fe's GP39-2s were of the Phase III type, purchased for higher altitude work (where the turbo helps make up for the thinner air, just like in my sports car :)). There was even an article many many years ago in MR on modifying an HO engine for the Phase III GP39-2. Search the back issues for this article (and maybe order the back issue if you want to perform the mod, or see how much is involved).
Then there are the normal differences between the initial GP38/39/40s, and the "dash-2" GP38/39/40s. It differs according to prototype, but some of the more common details to be included on the "dash-2" engines are:
-small oval window in a door on the engineer's side, under the radiator section.
-new truck design with "shock absorbers" on the end of one axle per side.
-electrical box behind the cab on the fireman's side.
-rear cab overhang, and shorter intertial intake section to make room for that overhang.
-lotsa internal upgrades.
Fans and radiator screen configurations, nose length, vent locations, light configurations, etc. differed between prototypes also, so check on prototypes for that.
---jps