You'll need to resample it from 48kHz to 44.1kHz.
When I've done this in the past I've demuxed the audio by ripping with DVD Decrypter. Then I convert the AC3 to WAV using BeSweet. Then resample the WAV. Can't remember if BeSweet does this or if I used SoundForge....
Anyway, for splitting tracks on sector boundaries (to avoid clicking), nothing is easier than CDWave.
Good luck.