Derek --
I'm pretty clueless about specific brands (I understand that the ones I use are no longer even being manufactured) but I can offer some generic advice that might prove useful.
As others have said on the bbs, the way to upgrade a system is from back to front -- that is, start at the speakers and work your way back to the head unit.
If you are planning on listening to your stereo as opposed to competing in SPL contests where the only objective is to produce the maximum number of decibels (I have no quarrel with those who do that, it's just not my thing) you do not need boxes full of subwoofers filling up the whole back end of your car. I (and others I have seen) have gotten quite good results with a single 10" subwoofer. You do need this as a minimum, though. A car stereo system without a subwoofer is like, oh, I don't know, insert your own cliche here. The improvement in sound quality and enjoyment is beyond description.
The more different sized cones you have making sound, the better balanced your sound spectrum will be. My personal recommendation, for what it's worth, would be a pair of six inch speakers in the doors, a set of four inch co-axials (or a pair of fours with separate tweeters) in the dash, a center channel 5" or 6" if you can fit it in, and perhaps a pair of six inch rear fill if you can mute them down enough that they don't pull your sound stage too far back.
The one specific brand I can whole-heartedly recommend is for the four-inch co-axials: The MB-Quart RKB-100 speakers are impressive, not to mention expensive ($250--$300 for the pair).
Amplifiers... again, you don't need kilowatts of power. My car gets by quite nicely with 150 watts. If I were a true, dedicated audiophile I would probably want 300 watts -- you get better transients, can run the amp gains lower. However... this is entirely preliminary, but I installed my Mark II empeg in my car last night, and those 4-volt audio outputs made a big difference feeding my existing amps -- much tighter, faster transients, more aggressive attacks in the treble range, and I had to back my amp gains down by about 40-50% in order to get the empeg up around its 0dB optimum setting. What all this means is... get a nice five channel amp in the 150--300 watt range, chances are the more money you pay the better the quality will be. Don't confuse more power with more quality. A $300 300-watt amp is likely a better amp than a $400 600-watt amp.
When it comes time to do the install, take your time. Look at all the possible different ways of doing things, and don't necessarily take the easiest or cheapest way out. A couple hundred bucks extra spent now will never be missed a year from now when you're enjoying your stereo.
Hope this gives you a little bit of help, at least steers you in a useful direction.
tanstaafl.
"There Ain't No Such Thing As A Free Lunch"
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"There Ain't No Such Thing As A Free Lunch"