There are applications built as part of the platform, with direct access (circumventing the SDK) to framework. Then there are applications that are built on top of published SDK.
In this case, your app is not meant for public distribution as a separate apk, given that you have a modified platform. If so, just build your app as part of the platform, and use your new interfaces in your app. You can use http://androidxref.com/4.3_r2.1/ to search the existing source tree, to see how the apps use the non-SDK interfaces as a reference.
If you are planning on publishing your app in Google Play, you should of course use only the public APIs, and you would not be modifying the platform to begin with.