Lots of interesting rail discussion here. I didn't go over it all with a fine-toothed comb, but some non-EMP-damaged locomotive sources may be...
(1) Hybrid diesel-electric
(2) the few extant steam locomotives, such as the Union Pacific Challenger, as well as museum exhibits kept in lovingly good order
(3) old-school locomotives that aren't as reliant on computers and electronics as the newer diesels
(4) newer diesels stashed by the government in sealed tunnels for just this sort of thing. (yes, I guess Morrow Project boltholes DO come to mind...)
In addition, EMP is likely to immediately shut down the entire modern U.S. rail network leaving hundreds of trains stranded on the rails, several miles apart, with no motive power. If you are able to somehow get a few modern diesels running and siphon diesel fuel from locos that are kaput, you might be able to pull the defunct locos off the stuck trains, pull them into a siding or shove them into a spur, then return to the train in question, bringing it somewhere where it can be put to use, stashed out of the way in a yard, or otherwise given space to unload into smaller vehicles (such as using a crane or pair of cranes to take the intermodal containers off so they can be unloaded or used for other purposes).
I can see coal plants being able to retool around EMP-incurred damage, and if they could receive coal from trains stranded on the main lines, they could contribute heavily to making a geographical area livable again. Going full-tilt-boogie, it takes a 120-car coal train a day to power a modest-sized modern coal plant.
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