That seems to have done the trick. MediaMonkey is a really good converter and it can rip CDs to FLAC directly unlike Windows Media Player. The only problem is that every time I open it, it makes itself into the default player and I have to go back into the VLC interface and make it the default again. Aside from that, it totally works. Thanks for the help!
EDIT: Fixed that problem too, so this setup is now literally perfect!