Based upon the few D&RGW 3000 series boxcars that I have worked on, I would say that neither the design of the wall framing nor the size of the lumber was changed at all during the 1920's rebuilding. As they exist now, in general, the cars have a mixture of old (dating from their original construction) and new (dating from the mid 1920's rebuilding) lumber in their wall structure. If it was reusable, the Rio Grande reused it!
As such, I would venture that the 1903 plans would be accurate for the cars after the rebuild, inasmuch as the wall framing is concerned.
The roof structure on the other hand is a different matter. Underneath the Murphy Roofs some cars retained their original wooden carlines (roof ribs), while many received new (at least to them) metal carlines. I have seen several types of metal carlines, most of which appear to have been cut down from standard gauge car parts. The wood in the "ceiling" of the car (ie the sheathing atop the carlines and beneath the metal roof) is 1x4 tongue & groove, which almost without exception, is reused car siding, perhaps even the 3000 series cars' original siding.
Jason Midyette