To start with the put-put-put problem first, a big muffler -- or even a couple of 'em -- will take care of that. I remember reading somewhere that tree thieves can drop a big veneer-grade walnut or cherry tree in your front yard at 3 a.m. using a chain saw fitted with a car muffler!
Maybe the HEP unit could be hidden inside the tender doghouse! (Just kidding.) There are units specifically designed to be slung beneath a railcar, and perhaps a couple of them per train could provide heat and light for the cars. Someone would have to calculate the current draw and design the circuitry. I have some info around here somewhere on these units, which I'll forward when I locate it. A $15,000 price tag sticks in my head. In our present-day litigious society, I wouldn't want to fool with coal stoves or propane heaters, and besides, with a generator, you could even provide power for laptops and cell phones, just like Amtrak!!