You might want to research EMP a bit more. Effects depend on what causes it and how close you are to the cause.

For instance, if it's due to a solar storm, the effect is more on grid-connected equipment than on everything. That's because the solar storm is less a pulse than an electromagnetic storm that induces currents in long conductors so it can fry major transformers and overload lines. The equipment damaged that way isn't generally in stock (it's big and costs a lot, so most places can't afford to keep spare inventory around). It would probably have to be built and shipped, taking weeks to months, so the grid would be down or crippled for a while. But it's unlikely that smaller devices would be impacted unless they're collateral damage of the grid effects. With much safety-oriented railroad gear being powered separately from the grid, it likely wouldn't have much problem initially (until the batteries run down or the generators run out of fuel). Unless you have an electric car and can't recharge it any more, you probably won't be without transportation as long as you can get fuel someplace (should gas stations have backup generators?).

A high-altitude nuke affects a smaller area than a solar storm, but potentially more strongly in that area. It would be a true EMP. Many smaller devices probably would be hurt by that, in addition to the grid itself. Of course, the radiation belts it leaves in orbit can wreck a lot of satellites, too - so much for PTC unless the GPS sats are really well hardened.

If you really expect somebody to pop a nuke in orbit that's big enough to take down the whole US, then we have a much bigger problem than just railroad effects. Either than, or your tinfoil hat needs renewing.