Here I am tomjohn
First off, the GP38-2 and GP39-2 ride on the same frame (59' 2" over coupler pulling faces) and share the same overall dimensions and many of the same components.
As for the differences, the GP39-2 actually went through several carbody variations, which are as different from each other as they are from a GP38-2.
Early GP39-2's are visually nearly identical to the earliest GP38-2's, with a two-piece wire-mesh radiator intake and fans spaced far apart. The main components of the hood (blower duct, dynamic brake housing etc) are in the same position on both models. The main differences are the engine room doors (2-3-3-2 grouping on the GP39-2 and 2-4-4 on the GP38-2) and the exhaust (single turbocharger stack on GP39-2, two exhaust stacks on GP38-2). Some earlier GP39-2's also had the fuel tank mounted farther to the rear, with a curious curved fuel filler pipe--this includes D&H and some ATSF units.
Early GP39-2, Reading version:
http://trainiax.net/drawings/36-emd/gp3 ... dg-ph1.gif
Early GP38-2, GMO version (this one lacks dynamic brakes, but it's the best comparison I have for the moment)
http://trainiax.net/drawings/36-emd/gp3 ... o-ph1a.gif
Few GP38-2's were built with the two-piece radiator intake, and after the earliest units, GP38-2's switched to a shorter single radiator intake and closer-spaced fans. However, the GP39-2 retained the longer two-piece intake for some time.
Later GP39-2's (BN and late ATSF versions) eventually adopted the shorter intake and closer-spaced fans of the GP38-2, as well as many other evolutionary changes ("phases") that were applied universally over the Dash-2 range. This includes Q-type fans on some units. They also received a large, flat exhaust silencer replacing the exhaust stack (as on other turbocharged models such as the GP40-2).
However, the biggest change in late vs. early GP39-2's is that the engine was moved over 3 feet rearward, taking the main air intake and blower duct with it. This leaves a large expanse of empty sheetmetal in the hood right behind the cab, and it places the dynamic brakes closer to the radiators. It also eliminates the last two tall hood doors, resulting in a 2-3-3 arrangement before the shorter doors under the radiator intakes begin.
Late GP38-2, BN version (this drawing also illustrates the nearly-flush, circular exhaust stacks of late GP38-2's)
http://trainiax.net/drawings/36-emd/gp3 ... n-ph2c.gif
Late GP39-2, BN version
http://trainiax.net/drawings/36-emd/gp3 ... n-ph2c.gif
The very last GP39-2's, built for the MKT, saw another cabody revision. They received taller two-piece radiator intakes and the engine (and blower duct/dynamic brakes) were moved forward a bit. The carbody is essentially that of the GP49 and it therefore has more in common with the GP50 than with other Dash-2 units. (I haven't drawn this version)
Regardless of the carbody variations, all GP38-2's have 2 exhaust stacks and all GP39-2's have a single stack, and both models have 2 radiator fans at the rear. You're also more likely to see a GP38-2, since it outsold the GP39-2 by almost 9 to 1.
Hope this helps!