All very good questions, which I am happy to answer.
The pipes at the end are in fact spinal-mount particle beam weapons, the retro-thrusters can be seen directly to left and right of them.

This is one of the eight primary shield generators, which are arrayed to give total coverage to the main hull. In an updated model I have independent generators on the wings as well.

This is one of the escape pod "docks", and there are of 16 of them, bringing the total number of escape pods to 80, with five pods per dock.

This is one of the four maneuvering thrusters intended for rolling, mounted on the upper and lower parts of the superstructure.

This is one of the two hangars, although I am debating whether or not to move them from the back of the wing to the sides of the forward hull.

These, of course, are the main engines. The structures connecting the two in the center and the structures on the side engines are part of the hyperdrive infrastructure.