Decryption is done with
Decrypt9
Can be done either on a cartridge (it will dump it to your SD slot) or an eShop install.
It does however require access to ARM9 side of 3DS, so either 9.2 FW with Homebrew Launcher or AL9H need to be available for you.
As for rebuilding, I used something called HackingToolkit3DS, which is kind of self-explanatory:
I'm guessing it's just a frontend for some command-line tools, didn't look into it though.
The whole process took me about an hour and a half -> 25 minutes each for decryption/encryption and 20 minutes each for transfering the files to and from PC with an FTP client.
We have a pretty extensive database of 3DS music rips, so I had the source music from the JPN release on hand - I'm guessing if you want to rip them on your own add another hour or so.