Regarding server... maybe some unscrupulous employee at the server host found the wallet and now makes an extended trip over the world.
If you didn't already know it then Ukyo founded a server hosting company long before bitfunder and weex:
http://www.cologuys.com/He might manage the server(s) himself. (it doesn't seem like he is involved in the company anymore though)
Why shouldnt he be able to use another wallet? The custom code isnt needed to send bitcoins.
Good question.. I have no idea but he wrote this definition of the custom code:
When weexchange started, bitcoind had no easy way to find out about new incoming transactions so we custom added sql code to it
There could easily be more custom code we haven't heard of though..