First and foremost, thanks to the many people that answered my stupid questions, offered their experiences, made suggestions and everything that made this install as easy as it was.
Secondly, this is how I chose to do my install and while I would love to hear suggestions or criticisms please do not take what is to follow as the singularly correct way to install a nav. Basically, use this information at your own risk.
Original purchase:
Purchased through crutchfield.com
- 099AVN5435 Eclipse AVN5435 CD/DVD Player with DVD Navigation
- 099SIRECL1 Eclipse SIR-ECL1 Sirius Satellite Radio
- 099RMC105 Eclipse RMC105 Infrared Remote Control for Car Audio
- 604RPL2YA ServiceNet 2Yr Replacement
- 120958202 Toyota Kit 2000-up, DD 2000-up, DD (free)
- 120701761 Toyota/Geo Wire Harness receiv receiver, 1987-up (free)
Total amount spent was $1,494.96 with a $40 off coupon supplied by Bill at crutchfield.
The AVN5435 in box:
Wiring Diagram:
Pretty simple stuff here. Just wire the wiring harness you buy to the 5435's wiring harnesses. In almost all cases the colors match but to be safe just use the wiring diagram and match it with the text on the wires in the 1761 wiring harness or on the instruction sheet.
Couple of exceptions to note (see: don't make the mistakes I did)
Factory Sub Be sure to connect the blue "power antenna" wire in the 1761 harness to the "ACC ON/OFF power supply terminal (blue/white) on the 5435's harness. Toyota jumpered the power antenna wire to power the factory sub. If you are hooking up your own sub skip this. Also, either find a corresponding connecter for the ACC ON/OFF wire or strip it to make the connection.
Sirius Sat Radio The sirius module's connection cable has 2 wires. One is yellow (constant power) and the other is black (ground). Be sure to tie these into the connections you are making between the 1761 harness and the 5435's harness. There are other ways to get power and to ground the sirius unit but I found this to be the easiest.
Feature Shut Off / Mobile Movies Not going to get into my thoughts on this, only to say that you are all adults, be responsible. Anyway, find the Red/White wire on the 5435's harnesses. It will also have a sticker on it identifing it as the "Parking Brake Signal". Tie this into the ground between the 1761 harness and the 5435's harness. If you are doing Sat Radio there will be 4 wires connected for the ground.

(note: this was before I realized I needed to ground the sirius unit)
All wired up:
Disassembly
I highly recomend downloading the factory XM radio install instructions as they detail the dash disassembly.
http://www.trdsource.com/Pictures/XM%20radio.pdf
First step is to remove the 2 screws on the bottom of the side trim.
Once the screws are removed lift from the bottom:
Once the side trim is removed you will see 2 screws, one on each side of the center trim piece.
Once these are removed, lift the center trim from the bottom to remove. Be VERY careful here, this plastic is thin and your climate controls are attached to it. Once you get it unclipped remove the 3 harnesses from the guages.
Now you will have access to the factory head unit. You will need a 10mm socket on an extention to remove the radio. Remove the 4 bolts and pull the radio out. Detach the harnesses and the antenna. You need to remove the mounting brackets to reuse for your install.
Place the factory brackets on the 5435 unit. The alignment indents will line up the correct mounting position.
Place the trim kit over the brakets and install. The trim pieces do not sit perfectly, they actually pull away from the unit. When you put the FJ's center trim back you can correct this.
Take a break and route the antenna wires. I installed both the Sirius and the Nav so I had two to run. Some have had sucess with mounting them inside, I decided to put them on the roof.
Place the antenna where you want it and use the channel at the front of the truck to run the wires. (per the factory XM install). Use tubing to hold the wires in place. You can get this at an aquairiam store or a hardware store.
sbechtold was nice enough to post pics of the factory install. I mirrored what he has, see link below:
Audiophiles and Nav Geeks
After you get these run and the plugs up to the radio area it is time to install the head unit and sirius module.
Here is where I mounted the Sirius unit:
In addition to the shared screw (see pic) I used the sticky padding that came with the unit and some elect tape to provide additional support. Be sure to hook up the sirius cables prior to mounting it. Luckly, I didn't make that mistake
Now plug everything into the 5435 and into the FJC. You just connect the wiring harnesses to the truck's harness. Plus, you need to connect the antenna (use the factory adaptor plug) and plug in the steering wheel control harness. (there is no adaptor harness needed, this is plug and play). Also, be sure to run the speed control wire (Purple/White) to the glove box area. You will need to remove the glove box to gain the access needed for the connection.
Now is a good time to turn on the truck and make sure everything works. Check FM/AM reception, NAV functions, Sirius Reception, etc...
If everything is good to go, bolt it back up. Be sure to adjust the trim kit peices as you place the center trim back on. (remember they want to bow out)
Time to connect the speed sensor if you have not done so already. FJ Lee provided the insight here:
Speed Signal Sensor wire?
And a pic of mine:
Antenna placement:
Unit Installed:
At night:
Totall time was about 5 hours but had I not stopped to take a ton of pictures and avoided some of the wiring mistakes it would have taken about 2 or 3. Not bad when you consider the sound shop I was going to use is 45 minutes away and they needed the truck for 2 days.
I tried to cover all I remembered about the install. Obviously if you have external amps, backup cameras, etc... then this overview will come up short. Use what you can and enjoy.