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Is there a program that I can feed it a large multi-game PGN and it can check each game for not only valid PGN format but also legal moves of each position?

Thanks for your time!
-Josh

Try using pgn-extract and joined available on Jim Ablett's site:

http://homepages.tesco.net/henry.ablett/jims.html

If comments (legal and not) are a problem, first use trim (part of 40H).