Here's what I did.
Bought a a scion T1806 Radio. Then went to the junkyard to find a wrecked TC that still had the IPOD wire. Picked one up at a pick and pull for 30 bucks. I was also lucky enough to find the IPOD and AUX jacks in the center storage console. I installed the radio with the scion ipod and aux wire harnesses. When you open the glove box, on the left hand side (not on the actual glove box drawer that opens, but the molding in the dash), there is a little plastic wall that hangs down. It doesn't interfere with the glove box drawer, and its not an essential piece as far as I know to the dash, so I cut a square hole and mounted the Ipod jack in there, so I can have my Ipod hidden in the glove box, while having the ability to control it through the head unit. I then wanted to mount the AUX jack in the center console next to my DAC button. So I routed the aux wire to my center console, took one of the spare covers out and cut off the ends and glued them to the AUX jack so it fills in the hole better and looks 'stock-ish'.
For my iphone I bought a car mount on amazon for cheap and put it up next to my steering wheel. I have a little stereo jack cord that I can plug in on the phone and run to the aux port on my console which essentially uses the car as a pair of headphones. Although I don't use the Ipod feature anymore because I now have my phone, my setup looks clean and like it came from the factory like that, which was important to me.
So heres essentially my parts list
Radio
Ipod wire (from radio to jack)
IPod jack, which connects to the Ipod wire to the radio
Wire harness (from toyota) that connects the jack to the actual ipod. Had to pick this up from partznet or the dealer... or maybe you can find it on ebay.
AUX wire (from radio to jack)
AUX jack