Agreed, wraps are a bad idea particularly on LD trains, but I was not thinking about wraps. More something along the lines of naming/nicknaming cars including mentioning that during announcements, and a few signs inside and outside the train. As for amounts take the EB it has about 10 cars not including the locomotive and baggage. If they each average 60K that's 600K, if you multiply that by the number of EB trainsets. That is not a small amount.
I think you're fantasizing a bit too much if you really think you can get $60,000 per year per car, and get every car "sponsored" on top of that.
Ad wraps are probably the only way to get any serious advertising dollars using the equipment itself, and even that wouldn't pull in anywhere close to $60K/year. Simply naming a car after a company, even with annoying sponsorship announcements by the crew, isn't going to sell for $60,000 per car, given the limited number of passengers that might be in any given car.
Just using your Empire Builder example, $600,000 per train times five trainsets (not to mention spare equipment needed) would be $3 million. Given the Empire Builder's ridership of between 500,000 and 600,000 per year, that's $5-$6 per person in advertising. Unless the people being advertised to are *extremely* wealthy and/or influential (given Amtrak's continued financial plight, that doesn't seem all that likely), no corporation would ever spend that kind of money for such a small target market (by comparison, according to Wikipedia, a 30-second Super Bowl ad averages $2.6 million, and has an audience of 90 million, which amounts to less than 3 cents per person).
All that to say, I really don't think there's as much money to be had as you are suggesting in selling advertising.