I just put a kenwood deck in my 00 Gt,omg what a let down. It sounds no where near as good as with the stock deck's. I guess I'll have to go after market in the spring. I don't even hear it that good at max volume whiledriving. Sounds ok when really car is off but that's no good.
Have a look again to make sure you didn't reverse the polarity on one of the speakers. I don't see why another head unit would decrease the souind quality that bad, since the amps are driving the speakers.
Not enough time to read through the post so if it has already been mentioned I apologize. I have an 02 vert with the mach sound system. Not the one with the actual sub in the back but I have two amps at least in the trunk and there are three ways to do the audio (and a fourth by not doing one way completely). See the last part? Thats what I did. I ordered a great pioneer head unit off of crutchfield many moons ago. However I didn't by the amp adapter specific to my car which they most likely sell for yours as well. All it is is an extra wiring harness that connects your woofer amp wiring to the units woofer amp outs. This makes a hug difference in sound because your using the system as it is electrically designed however you can just run the speakers on the hu without the woofers at all. Second you can gut it completely and replace it and if you want to upgrade old speakers its really not that bad of an option, besides older amps on ebay can be had next to nothing and if you know what your doing you can get great sound in a car for a fraction of the price of all the new units sold to you as a name brand unit with all componets. Third you can keep factory everything and just replace the speakers that need replacing but I would recomend the other two options over this one because Mach system well... Its great as a system but when you go for the cheap route of a mix and match system Mach is DEFINITELY NOT a team player. Do some reading on ohms and watts then check out the Mach system amp and speaker specifics and then search for the parts your replacing under a different brand (because mach system parts on ebay usually have crazy prices even though they are usually used and outdated). My option one without the plug and play harness ended up in me hardwiring the two door mids to the hu with speaker wire because they stopped working after a while on the set up for some reason and all I had were the old crappy mach tweeters i need to home rig a replacement for next. Have fun with it though, its all about the learning experience and trust me if you learn the mach system you could probably be an amatuer electrician!