All this concern about titling, vins, names, and other related items has already been worked out with the Camaro and Mustang bodies. All they would need to do is meet with Chrysler to work out the details and fees. However, I can't see Chrysler supporting a Cuda ahead of a Challenger or even Charger. Look at any of the Mopar Authentic restoration sheetmetal out there already.
Quality of the new bodies would be light years ahead of the originals. This has already been proven out with the previous offerings as well.
I don't see it changing values much at all on original cars. Clones may be another issue. The rare cars are rare because of their pedigree and option list. The availability of a "new" body simply makes it feasible for more builders to get into the game and be willing to build cars they wouldn't consider with an original car because of the value issue. That would stabilize the value of the clone car since it could be created with any number of new parts. Where that stablized value is would still be kind of high, I'd guess $60k or so for a turn key car. The beauty of repop bodies is that instead of dropping $8000 on a rust bucket that needs another $8000 worth of body work, you can get better foundation in a better assembly for the same $16k and then you can concentrate on the fun stuff like engines, suspension, and paint.