As far as I know, any major changes were done post production at the various modification centers, such as the Cheyenne Modification Center. Some of those changes were indeed at least in part structural but not in the sense that I think is alluded to above. And of course a lot of field modifications were made, some of which were incorporated in later versions some not so much.
Well for instance the tails were heavily altered as were the nose in some cases, involving more than just refits of equipment. These modifications often involved the removal of both skin and frame members, and reinstallation of modified frame members etc.
Actually these modifications were approved changes that were easier to do at mod centers rather than the factory. This included such things as the Cheyenne Tail, Chin turret, offset waist gunner's position, and interior equipment relocation, and some of these were driven by the receiving customer. I know Robert posted a link showing great photos of the mod center.
Bottom line - B-17s, whether they were produced by Boeing, Vega or Douglas were structurally the same. The only deviations you would have were repairs done at the factory known as "Material Review Board" (MRB) actions that were triggered by a manufacturing errors, and those actions were usually well documented.
Well for instance the tails were heavily altered as were the nose in some cases, involving more than just refits of equipment. These modifications often involved the removal of both skin and frame members, and reinstallation of modified frame members etc.