Well, the tank car's end beams were shortened a little, I don't recall by how much. I did it pretty much by eye. All these conversions were done about 28 years ago...
The caboose had a totally new underframe built and the streamlined cupola removed. (Gilbert's bay window caboose had both bay windows and a cupola.) But otherwise with the exception of some added details, there's no chopping and channeling of the bodies and they stand up pretty well against later stuff from the other manufacturers.
While Gilbert Flyer had some pretty accurate paint schemes, I also did some repaints. These are all straight Gilbert Flyer (except for the loco, I added the smoke deflector and boiler top air thanks to match the New Haven prototype,) posed on my scale railroad:
I did locate a comparison in my archives of a Gilbert boxcar and a former S Helper Service boxcar:
Bear in mind the Gilbert boxcar is based on the Pennsy X-29 boxcar, which was a relatively small car to begin with.
Rusty