Amtrak has baggage cars on at least some of its trains, and it seems you could use it meaningfully as a boxcar or even consider it to actually be a boxcar.
Another option for the fuel is to have multiple engines - many freight and some passenger trains already go around with multiple engines. You could probably just use one of the engines to hold fuel and siphon later, or just switch to that engine later when the first engine runs dry.
Amtrak also has boxcars which it runs on some trains (or, at least, has in the recent past). They offer a freight shipping service, and, in the past, carried mail.
Any but the very shortest freight train will run with multiple locomotives – two or three is a pretty common consist, and it’s not uncommon to see a long freight with a half-dozen locomotives. It’s much less common with passenger trains, since the load simply isn’t as heavy.
Another thing to consider is the fuel used in the hi-rail. Is the diesel used in diesel/electric locomotives the same as the diesel you buy at Exxon and put into diesel cars and trucks? If not, is it close enough that you could substitute one for the other (rail diesel in a diesel truck or road diesel in a locomotive) without causing catastrophic mechanical problems or significant loss of power or efficiency?
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Also worth noting is that locomotives have a “driver safety device”, a dead man’s switch, so normally the driver wouldn’t be able to leave the controls to go shoot at zombies or even use the restroom while the train is in motion. My understanding is it’s common or at least possible just to jam the pedal down though.
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The newer deadman systems require far more interaction than just putting something heavy on the pedal. They will periodically signal the operator to release the pedal momentarily, move the throttle, or some similar action.
[nitpick]No not the Chatsworth crash unless the engine block you are talking about was the on in the train that was traveling the other direction on the same track.
Did you maybe mean the Glendale metro link crash where the train hit a pickup truck?
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^You’re right; I was thinking of the SUV in the Glendale crash.
Don’t you think those could be overridden in the event of a zombie apocalypse?
For the most part, it’s the same stuff. The only possible rub is that at this particular moment in history, diesel engines on road vehicles are designed to run on ultra low sulphur diesel whereas locomotives don’t have to make the switch until something like 2016 (IIRC). So theoretically, if the hi-rail were based on a newer-model truck and the railroad was still using higher sulphur diesel, you might not be able to use train diesel in the truck, but you would definitely be able to use road diesel in the train.
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Don’t you think those could be overridden in the event of a zombie apocalypse?
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Hey, it’s a slippery slope. If you start letting them disable it for “zombie apocalypse” emergencies, they’ll start disabling it for “engineer needs a nap” ones too.
No, it’s not the same. The color is different, for starters (it’s considered off-highway and not subject to the on-highway federal tax). You recall incorrectly about the sulfur content of locomotives. ULSD was mandated this year. The Class 1s have been using it for several years.
And a full fuel tank in a hi-rail wouldn’t do much good in a locomotive. They have 3000+ gallon fuel tanks.
For starters and finishers. The only difference is the dye to indicate tax hasn’t been paid on it. Otherwise it’s just good old #2 diesel. While I’ve heard the tickets for using dyed diesel on the highway are pretty severe, presumably we can ignore them in this case.
Most locomotive and marine applications went to ULSD in 2012, but there’s still a whole slew of exceptions that aren’t set to expire until 2014 (according to here, although I swear I’d heard they were pushed out even further). Your chances of encountering it are fairly low, but there still is some non-ULSD diesel being used on US railroads.
But the multi-thousand gallon diesel tank at a truck stop could.
I’d think they would want at least one tank car filled with fuel in addition to the locomotive tanks. I think those exceed 20,000 gallons. They’d probably stop everywhere they could find fuel available to keep those filled. The OP isn’t talking about a huge train, or running at top speed, so they should be able to run for a month non-stop with a just one tank car in addition to the locomotive tanks. Find one tanker truck a week of fuel somewhere along the way and they can keep going forever. Well until the locomotive wears out. I’d think some kinds of maintenance would be impossible to do outside of a specialized facility.
Well that’s my point. 24.4 cents a gallon when you’re buying tens of millions of gallons of fuel per year is a pretty significant difference 
Ringling Brothers Barnum and Bailey still owns their own trains, which are mixed passenger and freight (including animals). There are some very interesting specialized train cars in private and corporate hands, though unless the circumstances were just right the author’s characters might have trouble getting to them…but it could make for some interesting story points.
I think that vigilance systems do have a manual override (in Australia at least) this is so that if the vigilance system fails enroute the train service can continue. however overriding this system involves breaking a seal that the driver can’t replace themself, so it is easy to discover if they have done it without receiving authorisation first.
Apocalyptically speaking, getting the diesel up out of the ground would be a lot of work sans electricity (nice tension builder). Of course, if the rails were sufficiently below the truck stop, siphoning would be an option.
I think those domed cars are getting to be uncommon, though I am not familiar with what gets used in the east. Amtrak long-distance stuff is all two-level, with very large windows on both sides, so defense would be pretty straight-forward. The observer car has a snack bar downstairs, but the downside is the lack of a poo-poo-place as one finds in passenger cars. You also need to find out what support fittings a passenger car would need to run its stuff (you can no longer see the track through the toilet) – with window glass and no A/C, death might be preferable to riding in the passenger car.
You also want to take into account that even though the couplings are there for connecting passenger and freight cars together, your passenger cars are most likely not going to have the right connections to have electricity or running water.
That means that your passenger areas are going to be a lot less cushy than otherwise. Not knocking cushioned chairs and carpeting, but the lack of heat and ac is going to be very noticeable.
