I cannot answer # 2, but can do so for # 1 and #3. Yes, Amtrak employees receive Railroad Retirement. The engineers ( and conductors ) are under the Hours of Service Law, which means they cannot be on duty more than twelve continuous hours, with various ifs, ands, and buts. On relatively short runs such as the Northeast Corridor,to my knowledge, an engineer would generally make one round trip, say, New York to Washington, with a break of an hour or two and then return to the home terminal. On long distance service, the agreement is that there may be one engineer if the assignment is six hours or less. If it is longer than that, or operates in the middle of the night, then there are two engineers. Examples:
On the Southwest Chief, there is a crew base at Albuquerque and the crews operate in both directions. The crews will leave ABQ midday and run the train to La Junta, Colorado, stay overnight in a motel, and return going west the next morning, arriving back home late in the afternoon of the second day. West from ABQ, it is a long assignment to Kingman, Arizona, where the layover is over 24 hours, which seems like a waste of manpower, but that is the nature of the schedule and the required rest period of at least eight hours. It would not be normal to carry extra crews while on board the train - perhaps that has happened at times, but would not count as rest. Under certain circumstances, such as a disruption in service, crews might be deadheaded on an other train or transported by road, or even by air. It is fairly common if a crew exceeds their hours due to a delay, ( going penalty ) the train will be halted and a relief crew brought out by road transport.