I would like to say I was just proving my point about online sources not being accurate, but I fell for spiffy presented data and you were correct....there is a 6" difference in the truck centers and overall length between the S1/S3 and S2/S4!
Here is a link to a source that should be accurate:
http://www.schenectadyhistory.org/railroads/manuals/tp107a/One would think the material and weight savings for making everything 6" shorter would not have been worth the effort vs. standardization on assembly fixtures and other parts, but it is what it is.
I am not sure that I would modify the mechanism and body shell for 0.0375" of length difference...even for an N Scale purist I am not sure the visual difference would be worth the effort.
Since you want an S3 I guess the trucks force you to use the Bachmann unit. The Atlas might be easier to start with because of the separate radiator grilles and two different styles.
Thanks for getting the discussion going as the conventional wisdom going back to the first ALCO switcher drawings was that the S1/S3 S2/S4 were the same except for the radiator and trucks.
Charlie Vlk