Hi just wondering if I could bypass the stock amp and sub and install a new one. Any help would be great!

Anything can be done, but if you're going through that much hassle you may as well replace the stock HU while you're at it.

Its really not very good, and new speakers and amps aren't going to help it produce any less of a muddy tone. Going the other way around would be better.

Somewhere, either stickied or by searching, you'll find a break down of the wiring diagram. The stock amp lives under the panel where a passenger's right foot would be (you can see the wires entering it if you pull the glove box).

You'll just need to pull the plugs from both ends and cross connect the outputs from the HU side to the side where your new amp wiring is.

I went the other direction: I replaced the HU with a new one, and it sounds infinitly better than the original in my 2004. I also ran a new all-in-wonder subwoofer combo in lieu of the original stock version, but that was technically uneccesary.

If you don't need processing, use the JL Audio Cleansweep. ($300)
If you do need processing, use the Rockford Fosgate 3Sixty.2. ($600)

I am debating with myself on if I want a high end audio setup, but if I decide I do, i'll be going with the 3Sixty.2 on the stock head unit to keep unsuspecting (theft) eyes at bay. :)

The other, more affordable option if you're just wanting a better sub is an RCA line out driver.

Just remember if you do maintain the stock headunit and eliminate the stock amp all together, you will need 3-5 channels of amplification. # channels will let you run all the inside speakers (left and right seperation only) on 2 channels and the sub on the 3rd. 5 channels will give you exactly the same set-up at stock. You can run the stock amp for the inside speakers and use the subout of the stock radio to drive a seperate aftermarket sub amp. What exactly are you trying to accomplish is the most important question?

I kept my stock speaker and head unit simply because my car is so new I didnt wanna change the look yet. I installed an mtx bass resoration factory sound processor that take the high pass and converts it to low pass, and also has several different gain controls and filter settings built in. Now in the back i have two kenwood 12" typhoon subwoofers power by an audiobahn intake series amp. What this gives me is i can keep the factory subwoofer, the factory amplification, and when i operate the subwoofer control on the head unit it controls both front and rear subs at the same time. I liked the operation of the factory set up im just a bug for boom, what can i say.

Where do you keep your groceries and ex-wives?