How much of the Shuttle physically existed in the simulator? Was it just the flight deck? Or were the mid-deck, lower equipment bay, and/or payload bay also included?
Note: there were a lot of training simulators. This answer concentrates on the Shuttle Mission Simulators. There were mockup type simulators like the Crew Compartment Trainer (CCT) that replicated the crew module interior very well. They weren't computer-driven though - most of the switches did nothing. Here's the CCT set up in a museum.
There were two different styles of "bases" or training devices in the two buildings that constituted the Shuttle Mission Simulator facility. Each style provided different parts of the Orbiter crew module for training.
The Motion Base (of which there was only one example) provided only the forward portion of the flight deck in a high-fidelity manner. In other words, everything seen and touched by the pilot and commander was flight-like. There were no aft or aft side panels, although the Display Electronics Unit (DEU) 4 and a keyboard was provided for the use of MS-1. This panel was not flight-like.
External view of the Motion Base
Internal view of the MS-2 and MS-1 seat positions in the Motion Base. You can see how the flight-like interior stops above and slightly behind the pilot and commander's heads. You can also see DEU 4 and its keyboard on the far right wall of the simulator.
The Fixed Base and GNS simulators provided a complete flight deck interior - forward, side, and aft crew station panels were all provided. They provided a mid-deck which was volumetrically and visually unrealistic but in which were mounted flight-like panels, lockers, and the galley. There was no airlock volume or Lower Equipment Bay volume simulated in these simulators, although airlock control panels were provided.
This is an exterior picture of the GNS (the Fixed Base was similar).
This picture shows how in these "bases" the flight-like interior continued past the pilot and commander seats. The left side wall is shown.
This picture shows some of the mid-deck panels with the unrealistic walls.
Before the GNS was retrofitted into a fully capable simulator, the Motion Base was provided with an aft crew station - but it was located in another room, and the Motion Base had to be locked in position, and an access bridge lowered.
There was a Waste Collection System (space toilet) simulation/training room in the facility, but it was not directly connected to any of the simulators. It was located between the Motion and Fixed Bases.
The payload bay was simulated only - you could see it out of the simulated aft windows, and interact with objects in the view.
Example of payload bay view out crew station aft windows
Picture credits: Either NASA PAO, or personal shots.
Reference: I worked there