WAV doesn't support metadata, so you will lose all that. ALAC does have metadata of course, but many of the PC packages (lie FB2K) that convert FLAC to ALAC lose the album art.
Try XRECODE II -- not free, but worth every penny. Fast batch operation. Easy to understand -- it is meant as a converter, not a full-featured player, so there is less to navigate. And the author responds instantly to emails. I give it 4 stars!
http://xrecode.com/
BTW, ALAC for an iPod has a max res of 48000, so you will need to half-sample your 96000 FLACs. XRECODE does this automatically -- I hear no audible difference.