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Athearn's kit is nearly perfect right out of the box.  With just a few quick Chessie specific details added you can have one of these big six axle units out on your pike.

Below is an actual pic of a real SD40-2.  It is a Dean Heacock pic.

How to make an Athearn SD40-2:
1.  Buy either an undecorated model or one that you can strip.  The Athearn Chessie paint job is not good, so I don't suggest buying one.  A powered model should cost you $20-25 on eBay and a dummy $12-15.
2.  SHELL: Shave off molded on grab irons with a sharp chisel blade.  Drill holes for all the new grab irons and the lift rings.  There are grab irons on the front of the nose, the right side of the nose, the top of the nose, and the back of the long hood.  All the lift rings are on the top of the long hood.  There are about 12 or so of each.  Also drill two holes on the top back of the long hood for the fan grab iron after you shave off the molded on one.
3.  SHELL: Sand off the small square with the three little posts on either side of the coupler.  This is the molding for the m.u. hoses.  There are two squares on the front pilot and two on the rear pilot.
4.  SHELL: Sand off the foot boards on the front and the back.  These are the protrusions at the bottom of the pilot where someone would stand to ride the locomotive.  Drill two holes in the front pilot to accept the Details West Chessie pilot.  Drill two holes in the rear pilot to accept the Details West rear plow.
5.  SHELL: While you have the drill out, drill each of the hand rail stancions so they are a little bigger.  They come just a little too small to fit the stancions right out of the box.
6.  CAB: Drill a hole centered on top of each of the six windows.  This will be where the windshield wipers attach.
7.  CAB: Drill out the holes for the handrails attach.  There are two on each side of the cab.  They are just a little too small to fit the wire right out of the box.
8.  SHELL:  Prime a Details West 5 Chime Leslie horn, the Details West Chessie plow, the Details West rear plow, a curved fan grab iron, 2 pairs of mu hoses, a side mounted bell, 2 uncoupling levers, and enough grab irons to fill all spots they belong (around 12 or so).
9.  SHELL:  Super glue in lift rings into the holes on the top of the long hood.  I don't prime these before I put them in.  Prime them carefully when the glue is dry.  Try not to fill the hole of the inside of the lift ring with paint.
10.  SHELL: Super glue on the Chessie pilot on the front of the shell, in the two holes you drilled in step number 4.  Also super glue the rear plow on.  When the pilot and plow are dry, super glue on the mu hoses.
11.  FRAME:  Shave off the four pegs that attach the frame to the shell.  Also prime the silver metal parts of the trucks with an enamel primer.  You will need to remove the plastic truck side frames to do this.  When the primer is dry, paint the wheel faces rust colors and the part behind the wheels black.
12.  SHELL:  Shave off the four holes that held the frame attachment pegs.  There are two of these on each sided of the shell.  Fill the small notch that is left with bondo and sand smooth.
13. SHELL:  Sand the "NW" lightly.  No need to get rid of it all, just soften the edges so that it isn't obvious it said "NW" after you paint it.  Remember this area will be covered with a decal eventually.
14.  SHELL and CAB: Prime the sides of the shell and cab light grey.  There is no need to prime the top or the frame since they will be dark blue.  The light grey allows for the yellow and orange to stand out better than a black surface underneath.
15.  FRAME: Put the truck side frames back on the frame.  Drybrush the fuel tank and the side frames with shades of grey and brown.  Overspray the side frames and fuel tank with a light dusting of railroad tie brown or another brown shade.  This will give it a nice dusty look.
16.  SHELL:  Paint the side sill and stripe SP Daylight Red.
17.  SHELL:  Paint the top of the hood, the walkways, the pilots and the top of the shell C&O Enchantment Blue.  This is quite involved and requires lots of tape.  It may be easier to to in multiple paintings.
18.  SHELL:  Spray the shell with Testors gloss coat and allow it to dry for a day.  Decal the shell with Microscale's Chessie locomotive set.  I used the Ches-C logo from one of the "Chessie System" decals for the nose herald.  The one given for the nose on the Microscale sheet is too small.  Also, the road #s are too small.  They should be the same size as the "B&O" letters.  I used the road #s from a set provided with my GP30 from the C&O Historical Society.  The builders plate came from another Microscale sheet.
19.  SHELL:  When done decaling, spray the shell with Testors Dull Coat and allow it to dry for a day.
20.  Prime the handrail parts and attach them to the shell.  I paint the parts that enter the shell so that when I paint the rest of the hand rails I don't get any paint on the shell itself, just the hand rails.  Paint them SP Daylight Red.
21.  Put in the "glass".  I just cut clear plastic the size of the windows and use white glue to hold them in.
22.  Assemble the shell and frame.  This will be tricky, since the couplers will need to be on the frame before you mate the two parts.
23.  Weather the model with an overspray with roof brown.  Center the spray around the bottom 1/4 of the locomotive.  Also, put some black weathering chalks around the exhaust on the top, the side sill under the battery box, and the louvers on the left side right behind the cab.  See photos for clarity.
24.  Attach the windshield wipers.
25.  You are done, enjoy your SD40-2.

Below is a pic of my SD40-2 in work.  Enjoy.

Below is a picture of the frame with the attachment pegs sanded off and the sides of the trucks primered.  You can see where the attachment pegs used to be.  They were right above the inside axles.

Below is a pic of the frame with the wheel faces painted.

Below is a pic of the frame completely done and ready to mate with the shell.

Below is a pic of the shell with the front attachment hole intact and the rear attachment hole sanded smooth with the side sill.  The front hole can be seen directly under the front edge of the long hood.  The small notch is all that is left of the sanded smooth hole in the back.  It is just behind the long tube that runs under the "NW" on the side sill.

Below is a pic of the shell primed and ready to be painted yellow.  No need to prime the top as it will be dark blue.

Below is a pic of the shell and cab painted yellow.  Up next, bondoing the holes on the side sill, and painting orange.

Below is a pic of the shell with the two mounting holes bondoed.  Carefull sanding will leave a rock hard smooth surface to paint.

Below is the shell with the SP Daylight Red applied

Below is the shell painted blue.  The louvers on the battery box have been shaved off, a black strip of decal will cover this later.  Also, only the front jack pad has been painted blue in this picture, the other one will be hand painted blue.  I was not happy with the stair well's yellow color, and will be touching that up before finishing this project.

Below is the SD40-2 decaled and ready for final assembly and weathering.

Below are some finished pics of the model.