Are you using your MBP? If so, you can use Max.
Apple - Downloads - Audio - Max
Preferences > Format > Available output formats > MPEG4 Audio > Encoder Settings > Available data formats > Apple Lossless
Then drag what you want to be converted and press convert. If everything is properly tagged, then you can just leave it on overnight and it'll be organized into folders. If they aren't tagged, you should probably do one album at a time and manually do it, or else it'll end up being like 1000 files titled x - jsdfhjklah that you'll have to organize.