hey man, i have a 06 tc and it shouldn't be any different.
installation is pretty easy. just color match and crimp all the wires together. there are some that are unused. vss wire is located on the harness behind the hvac and the reverse wire is located behind the glove box. go to scionlife.com and there is actually a guide that will help you. overall, installation is pretty easy. just make sure you have all the correct hardware like the brackets and the wiring harness. brackets on the oem radio will need to be modified in order for the door to fully close.
as for the ipod, you can use the aux port. only thing is you won't be able to control the ipod on the d3. so it's best if you buy the ipod cable.
anything else, let me know.