I've also tried asking about this here on BTCTalk several times, in this thread and Espers thread, but nobody even bothered to react to my questions. Except the Espers dev asking why I had become interested in ESP again.
Stay tuned, he'll get back to you when he catch up on all the questions.
Yes, BTC was where the trouble started, then those bitcoins were used in other markets and spreading the contamination. At the same time, normal trades occured, withdrawals, deposits, and so forth, shuffling the fake btc around.
After some days of investigation, and all users withdrawals, the damage became much more clear, and as it stands now 3.82 BTC, 270 LTC and 303951671 ESP is what is missing.
Best regards,
Bejjan