Its seems to me like the easiest thing in the world to work out where the coin is, even I have addresses that can lead back to Mtgox funds, but they don't owe me a Satoshi.
Beyond this I think people should post what they know about Mt. Gox's transaction system. Ie: limits, rolling funds from hot to cold wallets, withdrawal wallet sizes, etc.
For example my account, which was verified, was limited to 100 btc withdrawal, however upon contacting Gox support, they raised the limit to 300 btc. I only attempted one withdrawal exceeding 100 btc and that was in January, the transaction never posted to the blockchain and I was "refunded" the btc to my account following the halt of btc withdrawals. So I don't even know if > 100 btc worked.
Another example is that they have used various sized withdrawal processing wallets, these wallets always exhibit a pattern of transferring all funds to the withdrawer and to a new processing wallet. Now the problem with this is that some clients exhibit the same behavior. Additionally I've seen these purported withdrawal wallets just stop their pattern with sizable balances (500+ btc).
I find it hard to believe transaction malleability caused 744k in losses, the numbers just don't add up as many have stated. However if there were a bug in the software that lost withdrawal wallets, this could present an answer.
I'm partially done developing a program to do forensics on the blockchain to determine where possible losses occurred so any algorithmic info would be of help.