I hope you don't mind me linking to your photos. I will remove them if you like.
Photo 11 and 12 shows a mount for a drift sight which is normally mounted next to the Navigators cabinet close to the pressure door and under the voltage regulators. I wonder why they moved it there? You can see the original hole for the drift sight in photo number 13 below on the right side just aft of the turret plug. You will find that the screw pattern around the hole will likely match the one for the plexi dome which has been painted over with silver.
As for dropping of agents I heard that they used the tail turret opening for that. I have never seen documentation of it though. Nick Veronico has a couple of tail sections that were modified as target tugs but there is speculation that they may have been used for clandestine ops. One is all black and the other is natural metal. Agents could easily bail out through the aft entry hatch too although it is a bit small.
This photo shows a patch inside the turret well. The opening looks too small for someone to fit through. It looks like it may have been used for an additional camera or other special sensor.
These seats are very interesting. The seats and their location have eliminated the normal radar operators position. I wonder if the radar was completely removed or moved forward?
Photo 21 shows the radio rack that is commonly seen in surviving B-29's especially TB-29's that went through post war retrofit. As I recall this rack had an ARC-3 set along with the AIC interphone amp. There is a walk around oxygen bottle bracket mounted on top of the rack. All of the turret equipment and racks are all gone which seems to be typical of the post war mod aircraft.
The vents in the floor are normal as the turret computers were mounted under the aft floor and they needed ventilation especially on the ground in the South Pacific.
In the top of this shot you can see another of the post war mods typical of the TB-29's. It is the overhead radio console that mounted the control heads for radios so that both the pilot and co pilot could reach them. You can see the ARC-3 VHF head and the mount plate for the ARN-7 radio compass head.
These are the stock camera doors from the factory. They could be open up via a hand crank. The strike cameras took shots on the bomb run through these doors.
One of the other things commonly seen in the post war overhauled Superforts is the changing of the interior upholstery. This is when they went from the factory solid, non quilted, beautiful Army Bronze Green blanket to the more common diamond quilted upholstery called Skyfelt. Some of the survivors today have a mix of factory original and the Skyfelt as repairs would have been done with the later and readily available Skyfelt.
This shot shows what looks like parts of the camera mount may still be installed over the factory camera bays. It is unusual to see camera mounts in surviving B-29's. This mount looks quite high and could be locally fabricated. The higher mount would indicate a very long lens for high altitude photos.
I hope this helps,
Taigh