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1) Backup mods from your resources folder if you have any.
2) Use the game files extractor from "tools" (Rick's unpacker isn't needed anymore). All files will be in resources.
3) Rename the "packed" folder to anything.
4) Edit the extracted game files as you like (or put your modded files in resources, deleting the extracted originals).
5) Do not competely delete any extracted file (edits are fine), all must exist.
Now, the game won't find any packed files and will run the extracted one (so if there are some missing, the game might crash), including your modded ones. Achievements aren't disabled this way, however you won't be able to install LUA mods with this method (but it's irrelevant for music or gfx mods).
By any chance, can you link to a download for your game files? I can't live without the classic music :'(
All it is is changing the music.xml and the sound files.
The modded music.xml file wasn't made from the Afterbirth+ version, so it isn't compatible with Afterbirth+ at all (missing lines) and therefore crashes the game.
To fix it, you'll have to add yourself the few missing lines to the modded file. Open the .xml file with a text editor, and add this between the line with id 101 and </music> (at the end of the file):