The Stereo is mostly stock expect that I added a few things to it. It now sounds really awesome for a minimal investment.
First I added a 6 disk Changer by using a Blitz adapter and a Panasonic changer. They are both available through Crutchfield.com (my referral code is pkz0z-4t493-0hf2t), but at the time I bought them they told me it wouldn't work on my car; however I did some more research and found out that the stereo unit in this car is the exact same one as in other Toyotas that this application has been tested to work on.
The factory changer is basically a slightly modified Panasonic changer, and is used in most of Toyota's latter model cars that have the same basic stereo head unit. I've had it working just fine for years with no problems. (I'll have to find the exact model numbers for the adapter & changer that I used - but it ended up being much cheaper then Toyota Accessories Changer, and holds two extra disks then Toyota's).

Next, I had a sub woofer and amp left over from a pervious stereo system I had installed in my old Honda wagon. I spliced into the wires going to the factory amp located behind and to the left side of the glove box, and I ran a fused 10 gage wire off the battery for power.

At that point all I needed was a box, so I got a pre build box, from Crutchfield.com, as usual, and it all came together nicely. I also bought a 100mhz coil to filter out the high's, and mounted it on the box along with the amp.
This show's how I ran wires through the car buy pulling up the door seals. Here you can see wires for the amp signal, and CD-Changer. I ran power and remote wires down the other side of the car because it was more convenient and direct, and it kept the main power for the amp separated from the signal wires.

Here's a picture to show you the switch's I've installed for all my electrical wiring. The two bottom one's are for the stereo and come form a single remote power lead off the back of the stereo head unit. One is for the power antenna, and the other is to shut off the amp if I don't want it on at the time. The top two are for disabling the power windows and a blackout switch I made.

This is the wiring off the back of the stereo. You can see the red wire that taps into the remote power to go to the antenna and sub-amp. You can also see the thick yellow wire loom and associated plug that goes in the back of the head unit. It's from the adapter that runs the CD-changer, and also required a little fancy work to get power to it from off the stock head unit (a design flaw in the adapter if you ask me, but easily remedied)
Basically, the adapter wants you to wire directly to an accessary power lead, but neglects the fact that the stereo has a power lead that was designed to power the CD-Changer. I merely had to splice the wire for the CD-Changer power, into the correct socket in the adapters wire plug, and plug it into the head unit.

Here's a picture of the JBL tweeters I put in to replace the stock one's. It required making the stock speaker grill hole a bit larger, but over all it was a simple install (or at least after I figured out how to get the door panels off). The tweeters came with in-line crossovers as well, so they were a direct replacement for the stock tweeters and there respective crossovers.

Here's a couple of pictures of the power antenna, which was the last thing I installed. It also required a bit of work to remove the paneling out of the back of the car, and some manipulation to get it the stock mounting bracket to work with it. I also ended up with a lot of extra antenna wire in the wheel-well because I didn't want to try an re-run it, and didn't want to splice the stock wiring either. Over all it works well when it's up, and ok when it's down.

