The only external application you need is Visual Studio and a solid grasp on the fundamentals of graphics programming in C++. It will be extremely difficult to do, and depending on your coding skills will take a very long time to do, but yes it is possible.
If you don’t already know all the inner workings of the UE4 rendering code, or have never built your own rendering program using DirectX or OpenGL that is able to output high quality realtime rendering, I would advise against trying to make one right now. Get some good books on graphics programming theory and write a few small programs to understand all that is required to create a custom rendering solution. Once you have the fundamentals covered then start working on integration with the engine source, and build it from there.
But beware - This is a very difficult thing to do, you will need quite a bit of experience before you are able to re-create a rendering solution that will look anywhere near as good as the deferred renderer currently in UE4.
You can already create your own shaders, and you have the access to the source code so you can modify it to suit your needs. Replacing it outright is a huge task.