Crutchfield is your best bet if you have not done a lot of stereos before. I was able to get the head unit and adapter plugs from Amazon for a little less, but not significantly less. The hole is fairly deep so a lot of single DIN (traditional height and width) stereos will fit this car, but if you get it from Crutchfield, you know it will fit and the adapters will work.
I put a JVC in my daughter's '97 328 because she insisted that the orange in the stereo exactly match the orange of her other dash lights. The color of the display is almost perfect, but I don't much care for the head unit. They cram so much text into the tiny display that you can't read it, day or night, and the symbols on the buttons are microspcopic. Also, the bluetooth cell phone adapter is easy to use but sounds awful to the person you are talking to. Although the orange lettering matches, the super shiny black and chrome face stands out like a sore thumb and clearly does not belong in the dash.
Your door speakers are likely failed. Here are pictures of the problem but this suggested fix lasted less than a year
http://www.frontiernet.net/~papi/Speaker.htm
I replaced all the door speakers with Bavariansoundwerks speakers. They sound better than failed speakers but are not the amazing sound improvement that is claimed. I recommend them only because they are made to fit your factory speaker housings so they look stock.
You did not mention whether your speaker system is Harmon-Karmon. If so, you have a crappy HK amplifier under the trunk lining ahead of the left rear wheel well. The only good news is that it takes speaker-level signal inputs from your head unit so you can connect any head unit as though the amp were not there. The bad news is that HK amps tend to fail after 12-14 years, and they are custom made for this set of speakers with multiple crossover circuits inside. No other amp will replace them, and if you just bypass them with the signal from your head unit, you have to add $200+ worth of crossover circuits or disconnect half your speakers to keep from sending frequencies to your wolfers and tweeters that the speakers cannot handle. Also, the wires from the head unit to the amp are not really heavy enough to carry speaker load from the head unit if you bypass a failed HK amp. So far, however, it does not sound like your amp is failing so you don't need to worry about that yet. I would not suggest investing in new wolfers and tweeters, though, since there is a chance you will be disconnecting them at some point if you bypass a failed HK amp. I would buy only the door midrange speakers that have failed.