So I purchased a spare early GP38 w/DB shell for the DB.  My biggest concern was avoiding any seams that I would have to fill and sand.  With the small area I was working in, sanding down a filled joint would damage most of the surrounding detail.  So, I cut the shell and spare DB at the molded seam at the rear of the DB, and the top of the access doors.  Then I spent alot of time and care making the cut very square and smooth, to match up closely with the other piece.  After installing the new DB blister, I squared off the paper filter box with styrene strips and filler, and sanded down things down.
 
When I work on a joint, I brush paint it with undercoat (or in this case, the body color).  This gives me a much better idea of how much more work a section needs.  Otherwise, the different colors of different plastics and filler tend to fool my eyes.  It's a similar method to bodyshop workers using a guide coat.  In the shot below, you can see where I've painted the paper air filter box and DB area next to the PAF, to check how everything fits.  As you can see, I still need to add some filler to the top of the PAF to flatten things out.  This was not so evident before the area was painted.
For the bell, I used a Sunrise NS/SOU bell.  For the horns, I got two spare 3 chime horns from Atlas.  I carefully separated the small, rear-facing horn from the others, then turned it around, and carefully glued it in the same location, pointing forward.  I cut off one of the mounting legs, drilled one hole for the remaining leg, and glued a hornset on each end.  For walkway lights, I was initially planning on cutting some .020" strip styrene to shape, but I found that BLMA had produced etched walkway lights intended for mounting under the frame.  They come with very long, wide mounting tabs, which would require a huge gaping hole to mount them as they were, and they aren't thick enough to work on the hood.  It took some time to develop a method of modifying them, but I eventually got it.  I first filled the mounting tabs to a better size, and trimmed them down to a good length.  I then glued on a very small sliver of .010" strip styrene to the back of the etched part, and carefully trimmed it to match the shape of the light (and leave a lip on the front of the light).  Finally, I bent the tab perpendicular to the light, and mounted it in #80 drilled holes.  You can see one of the walkway lights directly above the handbrake in the photo to the right.
 
When one shaves off cast on details like MU hoses and uncoupling levers from the pilot, one can't help shaving off some of the tiger striping.  So after I shaved off those details, drilled appropriate holes, and rebuilt the coupler boxes to fit the Z/NN3 couplers, I painted the pilot black, and then added the tiger striping from Microscale's decal set.  I then added the modified footboards, JNJ MU hoses, and end handrail stanchions.
 
Then to emulate the electrical cabinet in front of the cab (next to the blower duct), I simply cut a piece of .040" x .100" strip styrene to length, glued it on, painted it black, and added a piece of decal from the same set.
 
Before cutting the frames, I separated them, and removed the motor, worm gears, and everything else, to keep the filings out of the running gear.  In the shot to the left, you can see that I cut the rear of the fuel tank weight up to the edge of the motor mount, which was pretty straightforward.  Then I cut the front portion back as far as I needed.  I then cut off the two motor saddle "pegs" (which snap the motor saddle into the frame itself) in that corner, and cut the fuel tank up to the bottom of the motor saddle.  I did this with a Dremel and a cutting wheel (the big, black, fiberglass impregnated, 2" diameter disk), regularly setting aside one half when it got hot, working on the other half until it got pretty hot, and going back to work on the first half.
 
 
Atlas produced a pair of high-hood versions of their GP38 in Southern Railway black.  And while this is a good start for me, I still want to correct some of the details according to prototype photographs (some can be seen here).
 
The surrounding pictures are shots of the model as it comes from Atlas.  While I'm keeping the paint job, the modifications I did are still pretty involved.  I need to change the DB, the paper filter box, the fuel tank, the horns, and the bell, all in addition to upgrading some existing details.  It turns out that modifying this high-hood factory painted engine required more work than the high-hood GP30 project.  The first thing I did is completely disassemble the model, even down to removing the motor and worm gears.  The only visible parts of this model that won't be modified or replaced are the windows and numberboards.  The next step is to shave off necessary details (like lift rings and grab irons), and drill appropriate mounting details.
 
The first thing I started on was the fuel tank, which requires some significant cutting of the frame.  Since these engines are rather light as it is, removing any weight is undesirable, but necessary.  If I find I need to get it back, I can remove the PC board, add weight to the top of the frame, and do a little rewiring.  And if I want to add DCC, I can use something like a gold mini, and still be able to add some more weight.  A lot of work, admittedly, but sometimes a little bit of weight can make all the difference.
 
Then I cut down the plastic fuel tank itself.  Instead of just lopping off one end, I cut off both ends, and shortened the center section.  This way, I kept a portion with tabs that lined up with the slots in the frame, and the tank simply snaps onto the modified frame as the normal pieces do.  Then I carefully rebent the copper contact strips in the front portion to clear the fuel tank.  Looking closely, it appears that I didn't get the plastic fuel tank short enough, but it's close enough to work for me.
 
Shortening the fuel tank means that I will have to redo the air reservoirs and piping.  That's not an issue for me, because I wanted to try and redo those items anyway, because I think the way that Atlas did them is a little awkward, and you lose the "shape" of the fuel tank.  I ordered a set of Sunrise air reservoirs, but the cast metal items are a little pitted, need to be straightened, and need mold parting lines shaved off.  I figured that by the time I do that, I can make my own out of styrene rods.
 
The next step was to tackle the DB area.  I wanted to resize the paper air filter box (that box that sticks up in front of the DB area on GP38s) and extend the DB blister, to match the prototype.  I cut down the paper air filter box, and started to trim the DB blister, so that I could extend it.  But at this point, I was unsure that I could do a good enough job scratchbuilding the extended blister.  To be honest, I do feel that if I worked at it long and hard enough, I'd get it, but I would also run the risk of damaging the shell.  I tried to come up with different possibilities, and I figured that I would get a better result if I would cut the existing DB blister out completely, and get the appropriate DB blister from another shell.
 
  So, I simply got some .080" styrene rod, and cut them to length.  To round the ends, I chucked them in a handheld drill, and turned it on a piece of 600 grit sandpaper, until the ends matched the shape of the Sunrise pieces.  I then added .0125" wire for air piping, .008" wire for drain lines, .006" wire for fuel filler vent lines, and cut up some .005" styrene for rear bracing.  For the fuel fillers, I cut some very narrow strips out of .005" brass sheet, cut them to length, and wrapped them around the ends of .025" wire.  This might not be the best representation, but it adds enough depth to it that it works for me.  I then cut the .025" wire to length, bent it, and mounted it.  Lastly, I cut more .005" brass sheet to size for the fuel level gauges near the fuel fillers.  Down the line, I intend to start tinkering with etching brass.  At that time, I hope to make a piece that will have the guages etched on it, but for now, sitting in the dark under the frame like that, this should be a decent enough substitute.
 
The next step was to add separate brake and sanding lines to the trucks.  The brake lines themselves aren't very apparent when the trucks are installed on the model (or from the angle which I took the shot).  But with the gaps that now exist between the trucks and fuel tank, the sanding lines make a noticeable improvement.  They were simply .020" wire formed by eye to varying shapes (like on the prototypes), and glued to the top of the truck frame, and right next to the bottom of the brakes.
 
At this point, I started adding some of the little details.  I filed down sunshades from the GMM kit to the small size close to Southerns shades, and added them, along with some wipers.  I removed the bell from the short hood (which is the wrong end), filled in the hole, and mimicked the sand filler with a very short piece of styrene rod.  I then added two circular vents by rounding off another styrene rod, and cutting the ends off.  I also started adding some of the handrail stanchions.
 
 
Then I moved on to adding the rest of the details to the body, which is where I find I need to keep myself from trying to rush things.  Now that BLMA has .007" thick grab irons (instead of .009" thick), I tried them.  While it's easier than bending my own out of .006" brass wire, the brass wire can be gently twisted and shifted to line things up, and make up for holes that aren't precisely drilled.  The steel wire grabs from BLMA aren't so forgiving, so they show my not-so-accurate hole drilling a little more.  I think I'll use them again in the future, though.  I also used BLMA lift rings for the first time.  While they are only slightly smaller than GMM counterparts, they are surprisingly much harder to handle.  But the effort is worth it, IMO.
 
My method for constructing handrails on this project is to add the stanchions, bend .008" wire for the handrails, ACC the handrails to the stanchions, and trim off the tops of the stanchions where need be.  While the results are okay, IMO, I could probably do much better by carefully soldering the wire, and bending the lip of the stanchion over, which is the traditional manner.    I avoided this before because my results weren't too good, but I think I've attained the skills to have a go at it next time.
 
Lastly, I added a speed recorder, and the uncoupling levers.  Then I painted the details, and did a light bit of weathering.  Most of the weathering disappeared when I sprayed on the dullcote to seal it, but being new to weathering, it's a learning experience, and nothing was ruined.  I will weather the engine more later on.  For now, the dullcote takes the edge off of the shine.