I just did this install in my 2005 w/ JBL. Here's what you'll need:
PT546-00120-AD Antenna Adapter- (You'll only need the part that plugs into the antenna)
PT546-00120-CH- Accessory Harness Adapter- Steering wheel controls, etc.
Metra TYTO-01- Converts the analog output of the head unit to the digital signals the Synthesis amp is looking for.
71-1761- Reverse Wiring Harness- Allows you to plug the converter into the Scion head unit without hacking up any vehicle wiring.
Optional:
PT546-00120-US- USB/Aux Adapter
PT546-74120-MC- Bluetooth Mic, but also necessary to enable bluetooth functionality for A2DP streaming.
The install was fairly straightforward once I figured out I needed the "reverse" harness shown above. You have to solder the reverse wiring harness to the Metra converter, but it's just matching colors:
One other odd thing to keep in mind. The "amp" label in the JBL Synthesis system is somewhat of a misnomer, it's really more of a controller. When you remove the stock head unit, you HAVE to center the fade/balance, turn bass/mid/treble adjustment to zero, and turn the stock head unit to MAX before you disconnect the battery. Because the head unit in the JBL Synthesis setup does not control these functions (the "amp" does), if you leave them low, that's now your new "max" values.
Other than that, you'll also have to deal with the poor fitment with the bezel, if that bothers you. The JBL head units are a different shape than the normal ones, so the Scion head units don't fill up the bezel quite as well. You'll either need to source a non-JBL bezel or make an adapter ring.