main.m:9:9: fatal error: 'UIKit/UIKit.h' file not found
That means that the UIKit headers can't be found. Do you have the iOS SDK installed somewhere? Have you configured the search paths in your makefile (or build environment) correctly?
The easiest way to start investigation is to start with a working Xcode project, compile a single .m file, and then see the command line that was used to compile that file. The clang rewriter takes slightly different options, but the search paths and a lot of the other configuration are the same.