Project Rewrite: Daleks in Manhattan

This may be a short-lived series, but I've been analysing the things I watch more critically in recent weeks and I'm starting to look at the stuff I don't like and wondering how I'd write them so I like them. Today I want to look at an episode from David Tennant's run as Doctor Who: "Daleks in Manhattan".

A brief rundown of the plot: Martha and the doctor arrive in Manhattan, 1930. Learning of strange disappearances throughout the city, they arrive in a shanty town to look for clues and end up taking a job in the sewers to further investigate. This leads to their discovery of the pig-men, human-pig hybrids created as a slave army. Shenanigans follow: Martha is kidnapped by pigmen, the doctor discovers daleks are in the Empire State Building (still under construction) and the short-lived reign of human-dalek hybrid Dalek Sec begins. It's a two-parter which ranges from shanty-town Hooverville in Central Park, to the city's sewers, to the top of the Empire State Building, and in general it feels unfocused and confusing.

So how would I fix it?