Ah, so what we're compiling is not just the plugin, but a branch of the entire engine? In that case, here's how to install it, for dummies like me:
1. Download only the three dependency packages (Optional, Required_1of2 and Required_2of2) from
Epic's UE4 Github page here.
2. Download Allegorithmic's source code from
their github page here.
3. Create a new folder on your computer, and extract Allegorithmic's source into that.
4. Navigate to the root folder, where you'll find the "GenerateProjectFiles.bat" and ".command" files
5. Extract the three dependency packages Epic provided into that folder.
6. Run the GenerateProjectFiles.bat (if you're on Windows) or .command files (if you're on Mac) to create Visual Studio solution files
7. Make sure you have Visual Studio installed. VS Express 2013 is available for free online from Microsoft, and you'll need it to compile this stuff.
8. Double click the .sln file to open it in Visual Studio. Wait for it to load everything.
9. When it's done and ready, go to Build -> Build Solution in the menu, which will start compiling the Unreal Engine. This could take a while.
Now, basically, you're done! You've just compiled the entire Unreal Engine, with Substance support built in. Open the editor by navigating to the /Engine/Binaries/[YourPlatform] folder and open UE4Editor.exe. Then just enable the Substance plugin in the editor's plugin manager and restart the editor, and you're golden.