I finished implementing nus3bank downloading into Brawl Custom Music. I have it set up so that you can select which song you want to replace, and it'll automatically rename the download for you. I'll add sorting by stage, menu, Smash Run only, etc. later. I'll show an example. Let's say we wanted to put Tales of Symphonia music over Dark Pit's theme (Lloyd Irving for Smash!).
On a song page, choose "Super Smash Bros. for Nintendo 3DS" from the "Download or add to template for" menu, and then choose whatever song you wanna replace. A "Download NUS3BANK" link will pop up under that, and you're good to go. I'll add something for people to build custom lists later. Let me know if you guys have any questions, and I'll be happy to work with someone for an offline converter at some point. My method is BRSTM->NUS3BANK.
P.S. I added Wii U support as well.