B44NYC already said it, but you're going to have a tough time putting the Bachmann interior inside the Walthers car. Though--funny enough--the problem isn't that the Bachmann base is too wide; it's that the Walthers one is too narrow! I'll spare no criticism of the new Bachmann Amfleets for their half-assed retooling and atrocious paint detail, but credit is due on the shape of the cars. The Bachmann Amfleets in all iterations as well as the earlier Metroliners have the correct shape. The Walthers cars curve too far back inward around the car floors and MU receptacles and are a fraction of an inch too narrow.
Anyway, while I wouldn't bother trying to make the Bachmann interior fit the Walthers car, what I would suggest instead is to save the Bachmann guts to get an idea of how to implement a lighting system or pickup for marker lights in a car and get some .030" styrene, HO-scale seats, and paint to make your own interiors.
Here's a site that shows basic Amtrak interior diagrams. Just a warning, something looks off about the Amfleet cafe interior as I'm almost certain that all the booths line up with the windows in an Amfleet I cafe, but I don't know what the prototype is for the diagram (probably an Amfleet II). Anyway, these diagrams give you the spacing for the seating as well as how they line up with the windows plus details showing spaces for luggage racks, bathrooms, electrical cabinets, etc. Precision Scale Co. makes perfect seats for interiors that are pretty cheap. I used some of them for a
Viewliner interior last year and have lots more for my own Amfleets and future commuter projects. Make some styrene of appropriate height to divide up the car (bathrooms, vestibules, luggage racks...), and if you want to get fancy, try even making some styrene strips to represent the overhead luggage racks. I've been toying with how I'd want to light car interiors myself--say with LED strips on top of styrene shaped like the overhead luggage racks to simulate the indirect lighting in the cars--but I have no experience with the electronics behind lighting, so I've been trying to research that and read up before investing in the various lights, resistors, wire, decoders, aspirin, et cetera.
Also, since you're interested in marker lights, take a look at
this as a guy from the Atlas forums did custom marker lights for his Amfleets. That might be something good to check out, and--with a little handiwork--a nicer effect than Bachmann's setup which illuminates way too much.