Now for a few notes on the other run-throughs mentioned.
The Sunset Limited has run through New Orleans since April, 1993, when it became the first regularly scheduled transcontinental passenger train in US history. From what I have been told, Amtrak's policy over the years has varied as to whether passengers were allowed to remain on board during the layover. Since I have never ridden through New Orleans on the Sunset (I got off there once in December, 2002, and boarded there this January), I can't speak to any of those policies from personal experience.
However, New Orleans is a pretty major service point for the Sunset (engines are changed there, and I think at one point OBS crews may have changed there as well). For all intents and purposes, the Sunset Limited through NOL is/was like the Capitol/Chief run through was originally meant to be. Now, the eastbound layover is extremely long (about 6 hours, give or take) because of the absolutely atrocious timekeeping that train has suffered at the hands of Union Pacific (not that CSX handles the train any better, of course).
From March, 2004, to February, 2005, the train arrived at its endpoints fewer than five times total during that period. Clearly something had to be done, but Amtrak's options were quite limited. Therefore, they settled on the policy of stretching the schedule to accommodate the numerous delays throughout the route (which has resulted in the OTP for the route skyrocketing from 1.something % up to about 25%).
The long eastbound NOL layover is simply an anomaly that results from a train whose arrival time cannot hope to be predicted with any degree of accuracy. There would be no benefit to making the train two separate routes, split in NOL, since doing so would require even more equipment (which Amtrak simply does not have . . . *period*).
For those wondering the status of the Capitol/Chief run-through, it only happens westbound. Eastbound, the Chief arrives in Chicago, and spends the night there before heading east to Washington the following day. In fact, I often wonder why Amtrak even bothers with the run-through any more since it does not save any equipment vs. having each train use its own captive sets, and a late Capitol Limited arrival almost always guarantees a late Southwest Chief departure (Chicago would have more time to service the Capitol Limited equipment to send it out as that night's #30).
As for the New York run-throughs, things are a bit more complicated. I had a book somewhere (which was a few months old) that noted the equipment turns, and while I don't recall offhand exactly what everything does, I will note that the run-throughs aren't quite simple (at least, they weren't back when that book was in effect). Essentially, a trainset (assuming it would stay together without ever being broken up for bad-ordered cars or whatever) would wind up running every single-level long-distance route (except the Cardinal) over the course of a week or two. This was done (and probably still is) because the Viewliner maintenance base is at Hialeah (Miami), and so Amtrak must rotate the Viewliners down there regularly. Therefore, the Lake Shore turns to a Florida train after spending the night in New York, and something else (either the Crescent or another Florida train) turns back to the Lake Shore.
:angry: 
