Man, sorry about this issue, I hope you get the 100% of your coins, but at least 55% would be a lot more than I have seen so many users not get when other exchanges went down. Good on BTC-E for at least trying, they are one for originals in the Bitcoin game from the beginning, so it was sad to see them go down at all.
Going to type this out not for you, as you already know, but for anyone else, DO NOT LEAVE YOUR CRYPTO ON EXCHANGES! Crypto currencies on these decentralized blockchain systems have one of their biggest benefits hindered once you leave the control of your coin to someone else. Just think on it. If you do not want to hold all your Bitcoin or Steem or whatever coin yourself, then stop using it and just leave your fiat cash in a bank. For everyone else, start using things like http://bitsquare.io and other decentralized exchange options as they become available.
Normally I leave it on my own wallet but I wanted to trade. Just really bad timing. Most of my coins are in wallets I control though. I know there are folks where this was not the case which is very unfortunate.