First off, a huge thanks to those who helped me choose the setup and helped teach me how to install. This was my first sub/amp install, and everything went smoothly after a lot of help from some of you. Thanks!

After seven years and 130k miles, the stock JBL sub in my 4runner finally let go. I love some bass with the music, but just clean/audible bass. So, I chose to replace the stock JBL sub instead of just adding another (also didn't want to loose cargo space). I did a lot of searching, and I found several real good threads, but most I found never showed the end result. So, I'm gonna try to sum up my findings and my install in this post, maybe it'll help someone else out.

First up, specs on the stock system. The sub is a 8" JBl with 2 ohm dual voice coils. The amp puts out ~90 watts max, estimated 45 watts rms. The stock sub is ~3" mounting depth.
Second, I chose to replace with JL Audio equipment. I've always heard good things about JL, and after the install I see why, very impressed. I went with a JL 8w1v2 sub (150 watts rms) and J2 250.1 amp (puts out 175 watts rms).
Third, wiring. I tapped into the rear DC outlet for my turn on wire. I tapped into the speaker wires right before entering the sub box and connected to my speaker level inputs on the amp. I cut out a spot on the box and added a speaker terminal plate for easy and quick connection. I did this directly behind the amp, mainly just because it was the only place I had room. I used the bolt for the seat to make the ground. I ran the power wire back, then across the firewall, in through a factory hole. I ran all wires down through the trim, then under the carpet and out in the cutout for the air vent under the passenger front seat.
And fourth, here are a few threads that really helped me out.

EDIT: It looks like the web site I used that showed how to access the sub is no longer working. I do have this process saved in a word file, if you need it PM me your e-mail and I will send it to you. Dannyg did the install and also has a writeup, which can be found here.

JL Audio - Car Audio Systems
And several more that gave me specs on the stock system, don't have links to them.
The end result sounds excellent. It's not gonna shake the car next to you, but it gives some great quality bass that was lacking with the stock sub. Let me know what you think, and just let me know if you have any questions.
Ok, so here are the install pics.
The equipment:

Stock setup:

Sub removed:

Sub comparison:

Modified box for clearance, sub liked about 1/4 inch fitting.

Sub installed:

Wiring:


Finished with amp:

Fuse holder:

Finished sub: