As for the vapor recovery system, all I can say is that it should be there.
As for the antenna, it's hard to say exactly what you can use without knowing what is left in your car. You should have a cable that goes from the radio to the c-pillar. On the c-pillar, the antenna wire should be connected to a small antenna module. There should be wires coming out of the module that attach to connectors on the edge of the side window. The antennae themselves are printed on the glass, similar to the defroster wires on the rear window. What exactly are they doing for the $400?
Your car should also have a small sharkfin antenna on the roof. It is actually a non-functional dummy antenna that fills the square hole in the roof. If you wanted to bypass the side window antenna, you could replace the dummy with a conventional roof mounted antenna. You would need the antenna base, a mast, and probably a couple of extension cables (to connect the roof antenna to the antenna wire at the c-pillar.