Any major brand CD player will out perform the stock unit. The most important thing it to make sure you get one with a high quality dampening system. Clarion, Eclipse, and Nakamichi are known for superb anti-skip dampening but others are equally good. Stay away from low priced Sony, Pioneer, Panasonic, etc. as they will not have the same quality. (High end units from these makers should do fine)
As for speakers let's start with the doors. This is one area where spending 500 buck isn't going to do much for you. With the door being basically an open cavern you can't expect too much from the 6" speaker. Find a component set with a really nice tweeter and passive crossover since this will be the only source for highs. The crossover will also prevent the 6" from over extending by trying to play too low. I'd say a 100Hz crossover point should work. There are plenty of great combos out there for $200 or less. I can point you to some web retailers who specialize in closeouts and you can save a bundle.
In the rear you have a totally different scenario. There are actually sealed enclodures back there which are perfect for subs. Only problem is that they are for 6" speakers. If you are not interested in booming bass you could install two long throw 6" subs in there. see
http://www.ddaudio.com, and have a nice solid sound from 55Hz to 100Hz. Anything below that will require a bigger sub.
As for the amp. Go with a four channel and bridge the rear two channels if you use the 6" subs. I chose a Lanzar Opti-Drive 4100 because of prior experience with them. I believe Alpine is releasing some new 4 and 5 channel amps that are close to the original amps dimensions and might be able to use a slightly modified factory bracket.
Now you need to hook it all up. Scrap the power and signal wires to the amp. Run a fresh set or two of RCA's and recommended size power wire. For speaker wire you might want to use the OEM wiring. Just remove the old speakers and unsolder the connectors. Place them on the new speakers (or on the crossover up front) and you're done on that end. At the amp just clip off the harness that plugged into the amp and use the diagram on the old amp to attach them to the new one. Unless you plan on putting 15's in the doors this will do fine.
Lots of people have diffrent opinions on this and it's your decision. You can always just price shop and buy the most expensive thing and it will probably sound good. Can you build a better sounding system for less? Absolutely. I competed in sound competitions for many years and when I bought my system for my own Viper I spent less than $500 (not including head unit and wire) and it sounds great. (Components in doors, 2-ways in rear, Lanzar amp, infinity basslink, lanzar active x-over) I do plan on scrapping the basslink and using the ddaudio 6" subs in the rear since I don't need the system to "pound".
Last thing... a sound system is alot like an engine. It needs to be tuned correctly to get maximum performance. Have a local shop check it out once in a while just to make sure it's "running right"
