I have to disagree with deg in that, the original E never made sense in terms of scale.
For instance the imagined layout of the interiors was based on aircraft carriers of the time. To fit the supposed decks in there you'd never have as high a ceiling as the interior sets did, and even then you're looking at nothing more than a plate of steel between each deck. I'm not sure what others imagine under the floor of a starship, but I imagine artificial gravity generators and all manner of conduits and access tubes to exist between each deck, and that takes up a lot of space that no one accounts for.
As for the shuttle set, it wasn't even full size. It was a 20' mock up of a 30' shuttle. Scaled to the accepted dimensions the Shuttle-bay is nothing more than a Shuttle-garage. Single car.
Vector, to figure out your scale I think should be easy. Figure out the basic size of an interior deck and everything accompanying it, and how many decks you want it to have (the same as the original I would imagine) and then scale the outside up to fit that in.