Edit: I ended up having time to test it. And it works fine. Thanks. :)

How to specify source for EmulationStation by making a custom module/package:

• In the terminal enter "sudo nano /home/pi/RetroPie-Setup/scriptmodules/supplementary/emulationstation-custom.sh"
• Paste the following code:

#!/usr/bin/env bash

rp_module_id="emulationstation-custom"
rp_module_desc="A modified version of EmulationStation."
rp_module_section="core"

function depends_emulationstation-custom() {
    depends_emulationstation
}

function sources_emulationstation-custom() {
    sources_emulationstation "https://github.com/retropie/EmulationStation" "master"
}

function build_emulationstation-custom() {
    build_emulationstation
}

function install_emulationstation-custom() {
    install_emulationstation
}

function configure_emulationstation-custom() {
    configure_emulationstation
}

function gui_emulationstation-custom() {
    gui_emulationstation
}

• Change "https://github.com/retropie/EmulationStation" to the fork you would like to use.
• Change "master" to the branch you would like to use.
• You can change the description at the top to anything you like and you can also change the name from "emulationstation-custom" to something else, note this must be reflected in all the function names as well.
• The rp_module_section value can be changed too but the only name for the other sections I'm aware of is "exp" for experimental.
• Press Ctrl+X, Y, then enter to save.
• Now when you build go to build EmulationStation there will be an option to build your custom version.

Note: The original emulationstation package/module will still say (installed) after installing your custom module. This is normal.

How to build EmulationStation from source:

• Now open RetroPie Setup in EmulationStation.
• Select Manage packages
• Select Manage core packages
• Select emulationstation (emulationstation-custom if you followed the later method)
• Select Update from source
• Now wait for however long it takes to compile. (This took 15 minutes on my Pi 3)

Temperature Warning:
Your Raspberry Pi can get pretty hot while compiling. A temp warning symbol will appear in the top right corner of your screen when the temperature reaches 75-80+ Celsius. The symbol appeared for me while compiling and I was not overclocking. I was using this case which has no real ventilation so it may not be a real issue for everyone.

If you're concerned and want to check what the temperature is:
Login to your Pi from Putty. (Enter retropie as the host name then hit enter. Login: pi, Password: raspberry). Then enter "/opt/vc/bin/vcgencmd measure_temp" to receive temperature readings.

• I'm not sure what to do if there were build errors when compiling, if EmulationStation still works from the previous installation then that's great. But I don't really have the time to purposefully build something that will fail to test it out.
• Now exit the RetroPie Setup app and restart EmulationStation for the changes to take effect.

Hope this helps others.

I dont know as far as debugging goes for building as each function is a piece of the build and the build folder may just be temporary (or may persist if it fails) I haven't looked at it extensively enough to test, I'm not as familiar with the code.

You can call each module function with retropiepackages as that's really what does all the work for the modules

• Do I fork the RetroPie fork of EmulationStation (if that's even possible), or the original EmulationStation? (I'm not aware if the latest ES works with RetroPie)
• Are all of the required libraries already installed?

So I just want to confirm, are these the steps you're talking about to build and point the module? And this is the correct directory to build in right?

git clone https://github.com/trigger-death/EmulationStation
cd /opt/retropie/supplementary/emulationstation
git checkout unstable
cmake -DCMAKE_CXX_COMPILER=g++-4.7 .
make

Edit: Also is there a way to debug this without dealing with the estimated multi-hour compile time?
Edit 2: Found this guide for compiling on Windows. This should do the trick for the above question. VS2015 takes forever to install sadly.