Unfortunately, that is a big problem. I am dealing with the same issue. I think you can now get all the cables, which you need three of to get from the head unit to the ipod, from Toyota dealers. They are expensive though.
Apparently, all 2006+ Scions come with the ipod wire that connects to the back of the HU, whether they have the ipod upgrade or not. I'm not familier with dealing with junk yards, but I'm going to try and find one around here that has a wiring harness from a 2006+ Scion. I wish somebody would make the connectors and sell them aftermarket.