Other than specifying a locomotive model, (GP 38), which was first built in January 1966, you have omitted sharing an important factor important to consider in recommending a paint scheme: what year are you designing your route (or session) for? Railroad paint schemes, even on short lines have changed over time. In general, over times, schemes have gone from more colorful and complex to ;less colorful, and simpler, to tending to more colorful and complex in recent years.
Generally speaking, though, short lines tend to be rather frugal creatures, and will generally keep their paint schemes as simple as possible, even going so far as only applying a "patch scheme", where patches of green paint is applied over all of the BN items, and the letters of the reporting mark applied over the green paint. But what I'd recommend is visiting short line locomotive pages of the railfan picture sites (like <
http://rrpicturearchives.net/railroadList.aspx?tid=3>, but there are others) and spend some time studying the locomotives pictured. You might find a scheme you like (or would like if modified "That would be really good, if it was in >color< and >color<.") but you can certainly look for general guidelines that applied to the design.
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