If you want to save space then don't convert to MP3. It's smaller than WAV but not the smallest size. Convert to AAC for the maximum quality and smallest file size.
As for a program to do it, use iTunes. Just right click on any song and "Create AAC Version". You can select multiple songs and convert as well.
As for invalid songs, iTunes typically just can't find them. You can select "search" and then once the file dialog comes up, in the search field (up top) just type in the song and it will be located. Or just sort your library via invalid types and delete if they are duplicates.
iTunes is a powerful program and over 8 versions has had many features added, so explore the menus and options, you can do just about anything with the program.
Frank
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