I'm going to say Snowfly's approach is a very good one, but I will also mix in a bit.
Ok the height of a building can be played with, there are a lot of factors and depends on what the building is for, this would dive too deep into architectural principles to really explain but as rule of thumb:
take the story height (space needed to live + floor and ceiling)
and multiply by the amount of stories, do watch for the start and top of a building and adjust for that. Also keep in mind your ceiling might actually be one and the same as the floor on the next level.
YES! Off course there is something like that, how do you think architects do that? There are book's like Neufert
Search for it on google, I've heard you can get by one quite easily.
I think it's done using a mix of a trained eye, proportionally form wise and to have a feeling for the dimensions of spaces used by humans and as Snow says the gameplay testing, where form follow gameplay rules.