Why convert from lossy to lossless? The resulting files will be anything but lossless and take up more space. I would re-rip that music if possible and not to WMA, MP3, or anything other than wave, then encode to FLAC. or rip "straight" to FLAC with some suitable program. To rip music, you might be able to use EAC in an emulation program, otherwise, I don't know.
If I remember correctly, you have to go with ALAC on a Mac, no? The difference is just that FLAC has slightly better compression. Both are lossless.