The "rational explanation" for nearly all the cost increase beyond inflation has to do with lawyers, Your Representatives in Congress and other legislatures, and infrequent orders.

Passenger equipment in the 1950s did not have to deal with ADA, shatter-resistant glazing, escape routes including pop-out windows and pop-up roof hatches, "crash management" systems for commute cars, and all the other stuff driven by laws and lawsuits. It would be illegal to build a car now like you did in the 1950s, or even the 1970s-80s (the Superliners have gotten quite a few updates over the years, and even so don't meet current standards in some ways). Locomotives in the 1950-60 era had no emission controls, no computers to make things "more efficient", no system calling home to the shop with a post-mortem after the engine has died, etc.; they also had less horsepower and used more fuel per horsepower-hour, and you needed a lot more of them (nothing excuses the P-40/42 series GEs though).

Also, there was an ongoing purchasing program at the private RRs that kept a couple of builders in business at a moderate level; once the system was cut back to bare bones and handed to Amtrak, there was no more continuing business. After a couple of big orders (Superliners, Amfleets), there was no more business for too many years to keep the manufacturers in business or interested. Govt operations are often like that for budget reasons: occasional huge orders when things get desperate and money is made available, then nothing for many years. Then of course when the time comes to replace or supplement the fleet you have to reinvent the wheel because the interested vendors have no history with the existing fleet, standards have changed, and of course the Olde Stuff is NIH for the people now in charge (all the people involved with the old stuff have retired).

Some large businesses operate that way too, especially utilities and others with long-lived assets. When it comes time to replace or do heavy maintenance on something, they try to sell it to somebody else first; if they have to do the work themselves the stock and profits take a big hit. The streetcar business was like that too: things were great until the tracks needed to be rebuilt; then many just folded and sold out to the bus folk or the operator of last resort (the govt).

Of course (back to the original post), this does sound like a contaminated fuel episode. They're not uncommon. However, if your truck or bus dies by the side of the road it doesn't block the rest of the highway or inconvenience a lot of people, and probably (assuming the engine didn't drink too much water) isn't horribly expensive to fix. Would some kind of water sensor have helped? Probably. But as long as the engine dies before the filter starts passing much water to it the overall cost probably won't be huge. Begs question: did UP have any (and how many) of its own locomotives fail due to the same contamination, assuming the bad fuel came from UP? And is UP's traffic so light that there wasn't some other train around to send a locomotive from and haul the Amtrak at least to the next station? I've seen BNSF power on Valley Amtraks (with the Amtrak loco supplying HEP) on a number of occasions.