This is just an opinion, but I have a very hard time believing that most rail transport will be more than an older diesel or steam locomotive with a half-dozen cars...maybe more, maybe less, but probably not more than a dozen at most for the first few years.
Most of the diesels you will see will be switching units including units taken from gravel pits, cement plants, and idle large industry, including steel mills. These will all be at least a generation old or older, dating back until the early to mid 1950's and some back until the WW2 era. These are all so crude that EMP will have little to no effect at all, are easy enough to maintain and tolerant enough of green operators that they are still in use today even in wide numbers in the US. They can burn the crudest diesel you can find, are light on the weathered track structure, and for what they are, maneuverable.
Steam locomotives will come from operating museums (think Steamtown in Pennsylvania) here and there....not many, and they too will be small to mid size units, but their contribution will be significant in those first few years.
The big diesels are common but most will be inoperative due to maintenance, high fuel consumption, high weight, and EMP damage. You don't need a 3000-4400hp diesel and all of its fuel consumption to move a dozen cars or so...maybe 800 to 1000 tons of car and cargo.
Bseides, until you can get people out to survey the condition of the roadbed and bridges along the routes used, you wouldn't want that anyway!
Where you don't have access to a locomotive, you'll see people use tucks in the 5+ ton range (or large airport tugs even) with wheel spacers, rigged flanges, and/or guide trucks. There will be plenty of scrap to take them from where you find trains in any quantity. A semi tractor or 10 wheel truck can pull 3-5 partially loaded cars at 10-20mph pretty well.
I see crews with such trucks pulling a couple of maintenance cars on the Canadian National every so often by the house here.
On that note, I can see local governments using people from refugee camps in the US to help with getting the rail networks back together after the war. I have photos of the Rock Island in the 1950's and with the exception of some drills and powered wrench rigs, the bulk of it was done with hand tools and sweat. On smaller scales, that's the way it's still done!
-Dave
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