He basically admits that he's been picking over both battlegrounds and boneyards to create these 1:1 replicas. He said that the Saucer Section of The Enterprise had to be recovered because of The Prime Directive. Apparently there was a native pre-warp species on the planet they crashed the saucer section onto, in ST Generations. The nacelles, pylons, and warp core came from the wreck of the NCC Saratoga (?). I suspect that would be the entire Battle Section of The Saratoga, since the Battle Section of The Enterprise was thoroughly destroyed. So that would include the main deflector dish, main engineering, the engine room, and something like 14-17 decks of the ship, as well as all their shuttle bays. The Captain's Yacht doesn't count as a shuttlebay, just a ridiculously fancy shuttle that they never used in the shows or movies.