This one takes the cake in my book:
2) In "Godzilla vs. Biollante," why is there a model and photos of the Godzilla from "King Kong vs. Godzilla" in the office if Showa series (with the exception of the first film) dose not exist in this timeline?
There are many theories as to why these objects appear in this film. One is the possibility that the first four Godzilla films; "Godzilla," "Gigantis the Fire Monster," "King Kong vs. Godzilla" and "Godzilla vs. The Thing," were all supposed to happen (Godzilla being finally killed by the Mothra larva). This might also explain why the people of Japan have knowledge of Godzilla after the Future Men "removed" him from time. The original Godzillas being two different creatures from the one in 1985.