I had similar problem with putting project to different markets - Google Play, Samsung, Amazon. All code base is the same, difference only in billing code.
The best solution I found is creating separate project for each market and pushing common code into library project.
In more detail, you need to leave common code in main project, make it library project and enable manifest merger for library and child projects. Add following lines to project.properties of main project:
android.library=true
manifestmerger.enabled=true
and this to project.properties of every child project:
android.library.reference.1=../testApp //absolute or relative path to your main project
manifestmerger.enabled=true
Also you need to attach main project as library in ADT plugin (in Eclipse - project properties -> Android) to all child projects. Main project manifest should not contain any launcher activity, it will be ignored, same thing with appWidget xml's and config activities, if you have some.
In child projects you can configure whatever you want and use main code by extending or just using needed classes as normal Java library. Also, you can use main project activities, services, broadcast receivers, etc just as they are in your child project without any duplication of manifest of child projects. After all configured, you can just build needed project for needed country as usual single project and you would have different apk's for different countries, as you want.
Here is more detail description of manifest merging http://www.platoevolved.com/blog/programming/android/merging-android-manifest-files/
Note, this feature was added in ADT version 20 preview 3.
Hope this helps.