Thanks to luna2 and ajenright for all the feedback in my first post. I wanted to come back with an update now that the install is done and share some info. I am really happy with how it turned out but it was an adventure getting there. I have some pics and wiring diagrams attached as well as some install experience to share.
Amp wiring:
There is an oversized grommet in the firewall on the passenger side with plenty of room for more wires, IF you feel like cutting it up a bit. I didn’t want to drill into a car with this many wires so I decided to perform a bit of surgery on the grommet instead. Not exactly kosher I know but I didn’t feel like making the walk of shame back to the dealer after drilling through a bunch of electronics. Peering through the existing hole I could see daylight on the other side so I taped my power cable to a metal rod and pushed it through. 17’ of wire just barely got me to the rear deck.
I found a nice ground in the rear strut tower mounting bolts after grinding the paint off the body with a dremel, and it made for a very short ground wire.
I have auto sensing amps so I didn’t run a remote wire but if I had, the easiest way would have been to grab the cigarette lighter power I think.
Speaker wiring:
I went with new components in the front. There is only about 2.5" behind the door before you hit window but, there is another 1.5" of space between the door and the door panel. I was able to mount a pair of Polk MM 6501's, which are almost 3" deep, to a bracket made of 3/4" MDF with plenty of room. I angled the tweeter a bit and put it at the bottom front where it could penetrate the door panel grill and the imaging is great.

The thing is, with an amp, I am running my own wires. And with components, I am running 2 sets behind the crossover, and with a door being a somewhat hostile environment (water etc) I didn’t want the crossover in there so that meant getting two pairs of new wire into the doors. Getting wire into the passenger door through the insanely long grommet wasn’t too bad, some stiff wire and silicone spray will do the trick, then tape your wire to the end and pull through. But in my case, some overzealous assembly line dude took it upon himself to tape up the driver side grommet tube so tight I couldn’t get a strand of dental floss through there. Pissed off and not ready to compromise at this point after having the other side done already, I took the door off. Note: taking a door off is easy, 5 bolts, three harnesses. Putting a door back on is HARD, without a buddy and a hydraulic jack. Follow best practices for disconnecting airbag systems (yellow harnesses)
The 6x9s in back were much easier. I just used the existing speakers as a guide and made some more adapters out of MDF for a pair of Polk DB69s:

I needed to route speaker level inputs to my amp. I found the easiest way to tap into the front channels was at the dash speaker - the grille front pops right out. Solder or buy a harness to tap in, it is a straight shot down to the floor trim panels. Just make sure you grab the leads that go to the deck – there are 4 wires in the harness but 2 go to the door speakers which are run in parallel. Just get some test leads and plug a speaker in to find the hot wires.
Watch out for the front kick panels, the plastic anchors are angled for some godforsaken reason. Take out the front nut and twist the top of the panel forward and the bottom toward the rear of the car – do not pull straight up.
For the airbag seat rests on the sides of the rear seats, undo the two bolts and the bottom and lift up. You don’t need to disconnect them.
The backseat comes out by pulling straight up to disconnect the clips underneath like every most every other backseat. On the rear deck, push the brake light assembly to the driver side and it will pop out.
Amp mounting:
The biggest problem I had was trying to find a suitable spot to mount a pair of amps even though they were rather small. The trunk is huge but if you look closely there are practically no flat surfaces large enough to mount an amp. If your amp is less than ~ 10" x 8" x 2" e.g. the JL HD or XD series all-in-ones, you can squeeze it in under the rear deck above the trunk torsion bars.
For half the price of one of those I scored a pair of Alpines on Amazon, an MRX-F30 and an MRX-M50, but I had a space issue as a result. I decided to make a shelf that would sit under the trunk torsion bars and mount the amps to it. Here is the backside:

And here it is with the amps mounted. I didn’t have to drill any holes, just used 3” bolts into existing unused holes in the rear deck. If you use nuts, be sure to put some adhesive around them so you can take the shelf out without pulling the rear deck apart. That chunk missing is so it fits around the middle seat belt assembly.

Here is the whole works installed. The only downside is it blocks the trunk light but the alpines have bright blue power LEDs that give the whole trunk a nice blue glow, hurray for unintended awesomeness.

I wasn’t a fan of the stock Display Audio with Nav at first, with its low-res resistive touchscreen and cheesy EQ, but it is actually a quality unit, made by Pioneer. It puts out flat signal and doesn’t seem to clip, though I have yet to test this. I put a $20 dollar 32GB flash disk in the USB port with my entire collection and it scanned all the ID3 tags in seconds, and I was on my merry way. There is zero noise, and the SQ is amazing. It was a fun project.
6 speaker with Nav wiring diagram
https://docs.google.com/open?id=0B_7agNvyljePWFFqZW5VZmVkUEk
10 speaker with JBL wiring diagram
https://docs.google.com/open?id=0B_7agNvyljePWEd1aW5vV1VqY0k
Slightly outdated Crutchfield MasterSheet (Gen6 2007-2011)
https://docs.google.com/open?id=0B_7agNvyljePenZwRmxVTmZtbkk
Enjoy
Amp wiring:
There is an oversized grommet in the firewall on the passenger side with plenty of room for more wires, IF you feel like cutting it up a bit. I didn’t want to drill into a car with this many wires so I decided to perform a bit of surgery on the grommet instead. Not exactly kosher I know but I didn’t feel like making the walk of shame back to the dealer after drilling through a bunch of electronics. Peering through the existing hole I could see daylight on the other side so I taped my power cable to a metal rod and pushed it through. 17’ of wire just barely got me to the rear deck.
I found a nice ground in the rear strut tower mounting bolts after grinding the paint off the body with a dremel, and it made for a very short ground wire.
I have auto sensing amps so I didn’t run a remote wire but if I had, the easiest way would have been to grab the cigarette lighter power I think.
Speaker wiring:
I went with new components in the front. There is only about 2.5" behind the door before you hit window but, there is another 1.5" of space between the door and the door panel. I was able to mount a pair of Polk MM 6501's, which are almost 3" deep, to a bracket made of 3/4" MDF with plenty of room. I angled the tweeter a bit and put it at the bottom front where it could penetrate the door panel grill and the imaging is great.

The thing is, with an amp, I am running my own wires. And with components, I am running 2 sets behind the crossover, and with a door being a somewhat hostile environment (water etc) I didn’t want the crossover in there so that meant getting two pairs of new wire into the doors. Getting wire into the passenger door through the insanely long grommet wasn’t too bad, some stiff wire and silicone spray will do the trick, then tape your wire to the end and pull through. But in my case, some overzealous assembly line dude took it upon himself to tape up the driver side grommet tube so tight I couldn’t get a strand of dental floss through there. Pissed off and not ready to compromise at this point after having the other side done already, I took the door off. Note: taking a door off is easy, 5 bolts, three harnesses. Putting a door back on is HARD, without a buddy and a hydraulic jack. Follow best practices for disconnecting airbag systems (yellow harnesses)
The 6x9s in back were much easier. I just used the existing speakers as a guide and made some more adapters out of MDF for a pair of Polk DB69s:

I needed to route speaker level inputs to my amp. I found the easiest way to tap into the front channels was at the dash speaker - the grille front pops right out. Solder or buy a harness to tap in, it is a straight shot down to the floor trim panels. Just make sure you grab the leads that go to the deck – there are 4 wires in the harness but 2 go to the door speakers which are run in parallel. Just get some test leads and plug a speaker in to find the hot wires.
Watch out for the front kick panels, the plastic anchors are angled for some godforsaken reason. Take out the front nut and twist the top of the panel forward and the bottom toward the rear of the car – do not pull straight up.
For the airbag seat rests on the sides of the rear seats, undo the two bolts and the bottom and lift up. You don’t need to disconnect them.
The backseat comes out by pulling straight up to disconnect the clips underneath like every most every other backseat. On the rear deck, push the brake light assembly to the driver side and it will pop out.
Amp mounting:
The biggest problem I had was trying to find a suitable spot to mount a pair of amps even though they were rather small. The trunk is huge but if you look closely there are practically no flat surfaces large enough to mount an amp. If your amp is less than ~ 10" x 8" x 2" e.g. the JL HD or XD series all-in-ones, you can squeeze it in under the rear deck above the trunk torsion bars.
For half the price of one of those I scored a pair of Alpines on Amazon, an MRX-F30 and an MRX-M50, but I had a space issue as a result. I decided to make a shelf that would sit under the trunk torsion bars and mount the amps to it. Here is the backside:

And here it is with the amps mounted. I didn’t have to drill any holes, just used 3” bolts into existing unused holes in the rear deck. If you use nuts, be sure to put some adhesive around them so you can take the shelf out without pulling the rear deck apart. That chunk missing is so it fits around the middle seat belt assembly.

Here is the whole works installed. The only downside is it blocks the trunk light but the alpines have bright blue power LEDs that give the whole trunk a nice blue glow, hurray for unintended awesomeness.

I wasn’t a fan of the stock Display Audio with Nav at first, with its low-res resistive touchscreen and cheesy EQ, but it is actually a quality unit, made by Pioneer. It puts out flat signal and doesn’t seem to clip, though I have yet to test this. I put a $20 dollar 32GB flash disk in the USB port with my entire collection and it scanned all the ID3 tags in seconds, and I was on my merry way. There is zero noise, and the SQ is amazing. It was a fun project.
6 speaker with Nav wiring diagram
https://docs.google.com/open?id=0B_7agNvyljePWFFqZW5VZmVkUEk
10 speaker with JBL wiring diagram
https://docs.google.com/open?id=0B_7agNvyljePWEd1aW5vV1VqY0k
Slightly outdated Crutchfield MasterSheet (Gen6 2007-2011)
https://docs.google.com/open?id=0B_7agNvyljePenZwRmxVTmZtbkk
Enjoy