After searching around on TL a few times for any information on people that have already done this, I decided to make my own thread since it seems un-covered. Also over at this thread people were asking how to get this done.
Today I decided to replace my Protoss music with the old Protoss music from BW, and was super happy with how easy it was and how nice it turned out.
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An mpq file is basically a folder system just like all the other folders on your pc. Blizzard created mpq files as a way to package together all their files, sort of like a .zip archive. So in order to replace any file with another within the mpq, you just need to replace an old file with a new one that has the same filename and file extension. You can open this mpq archive with an mpq editor (since Windows cannot do it alone), and then replace anything you like. Often times the files within the mpq will have odd names. In instance that this happens, you use a listfile which is a file that contains a list of filenames, so that when you use the mpq editor to open an mpq file some of the filenames have meaningful names.
To get started download an mpq editor from here. Be sure to use the proper listfile.
You'll also need the BW music files, which you can download here: BW Terran Music; BW ProtossMusic; BW Zerg Music. If you wish to replace other sound files, I suggest getting a copy of Brood War somewhere and extracting the music yourself. You can do this with the mpq editor and just opening the BW mpq, navigating through the folder system, and dragging out whatever files you want. It's really easy.
The music files for SC2 are found in StarCraft II/Mods/Liberty.SC2Mod/base.SC2Assets. Once you open this file in the mpq editor, navigate to Assets/Music. All of the SC2 music files are on .ogg format, which is just a type of sound file. I suggest backing up any files you edit before editing them, in case you mess up. We'll need to be able to convert .wav files ripped from your BW installation (or the ones I provided for download) to .ogg. I used wavepad sound editor for this, but you can use any program you'd like. If you want to use my copy of wavepad you can download it here, which is I believe the free version.
Once you have converted your .wav files from BW into .ogg format, just rename your converted files to the same name as the file in your SC2 mpq that you wish to replace. For example, SC2 has 5 different Protoss music files, so I took my three music files from BW and renamed them to the corresponding 5 in SC2 (I had my first and second BW file replace 4 and 5 since BW only has three Protoss songs).
Now make sure to close the mpq editor before running SC2, and if you did everything properly you'll hear your newly replaced .ogg files playing in-game!
Read this before replying! If you want to change other files in any of the SC2 mpq's, simply create a replacement file with the same filename and filetype, and replace the old file in the mpq with your new one. Here and here is some more information on this.