Can anyone track down the block that contains the deposit related to this sell? I assume we would be able to see the deposit to a Mt. Gox account in the block chain. Of course we can't know if it was a gradual deposit or a single 40,000 BTC one, or when it happened.
You can try...but it might be hard. You can import private keys to mtgox now, as well as use codes to transfer between accounts. You have no idea how long someone had funds in mtgox or if they got them from buying on mtgox in the first place.
Do any tools exist that can be used for working with the block chain locally? Can I, for example, somehow do a search in the block chain for a block containing at least, for example, 40,000 BTC worth of transaction within the last 7 days? That would be really interesting to be able to do.
yes, try here:
https://bitcointalk.org/index.php?topic=50721.0