What I did for my old GS300 is I purchase the dash kit, an Alpine amp to replace the stock amp because I don't want to go through the hassle of bypassing the stock amp or making it work on the after market receiver. I bought a JVC KD-G820 receiver of which I highly recommend that due to the fact that there are at least 5 preset EQ and you can set your own EQ too. You can find one on eBay for cheaper besides, they don't have it in the shelf at your local BestBuy or CircuitCity anymore. I tried looking for another one but couldn't find it and they say they won't be getting it anymore. I bought two of them just last week, one for my Evo and the other was by mistake but I put it in my wife's Corolla :D
It took me a few hours to do it myself... except I have to take out the stock CD changer and in the same place, I make my own bracket for the Alpine amp to sit in. I can't tell you how I did it but it takes a few hours and trips to the local hardware store to get some screws, nuts and bolts. I use the hex bolt from Ace. I did purchase the wiring harness but it didn't came to me in time so I cut the wires and hard wire it myself. Only do it if you plan to keep your car or won't regret loosing the deck when it's time to let it go.
You don't need to replace any speakers in the GS300 or 400 including sub unless you want your ear to blow. With the setup I have, it sounds real sweet. I just wish I took some pic of my work so I can show you guys but I traded that baby in for a Mitsubishi Evo. :chairshot:
I'm sure there's some threads in here that will show you how to remove your OEM stereo.