So one of my applications was rejected from the Amazon app store today. The reason was because inside my app, I linked to the paid version of the app on the Android market.
Just refactor most of your project into a Project Library, and then create multiple projects (e.g., for each app store) that have only unique icon and string resources, their own package ID declared in the manifest, and then a main activity that extends the main activity that you have defined in your library.
That way, all the unique URLs can be provided by overriding, in each particular app project's activity, the virtual or abstract methods defined in your library's main activity. The library code that that displays these URLs can obtain them via a polymorphic call to each of those methods.
That way, each such specialized project will be very small, and maintenance will be mainly to your library, as described here:
Multiple Apps with a shared code base