If youre looking to upgrade the speakers just forget it. I know this is going to be hard to swallow. But you would be better off just scrapping the entire system and getting a new deck, 4 channel amp with 2 sets of component speakers, and a subwoofer system. Heres my reasoning.
Ford/Mach Audio made the mach 460 sound system for the user to listen to at moderate volumes. Throughout the years they used essentially the same 1995 speaker technology. So the internal equalizer is always trying to compensate for the speakers imperfections by overloading the signal with bass and treble. Sure this sounds decent with the factory speakers at normal volumes, but turn it up loud and youll know what I mean. By adding aftermarket speakers you will only be making the problem worse.
Now my second reason is because of how messed up ford wired the system. Your system has 3 amplifiers. One operates the tweeters, and the others operate the woofers. If you were to replace the deck directly, you would only hear the sound through the tweeters. (A special wiring harness can take care of that). But then all your quality gained through a new deck is lost through the poor amps.
So you say: "alright, i will just replace the deck and the speakers, and use all the factory wiring" WELL then, best of luck to you because the amps will melt. Each tweeter and woofer is rated at 6 ohms. At the crossover (separates which frequencies are sent to the woofer or tweeter) the final impedance is rated at 3 ohms because of the parallel wiring in the crossover. Now most aftermarket component crossovers are wired in series with 2 ohm drivers to equal a 4 ohm final impedance. But if you are directly placing these aftermarket drivers into the factory wiring, then you will be giving the amp a 1 ohm load. Which is highly unstable and unsafe for the factory amps.
So lets say you want to use the aftermarket crossover to bypass the whole unstable load situation. But thats not possible because remember in the mach system, the signals coming to the woofer and tweeter are coming from separate sources, which makes using an aftermarket crossover impossible.
So ultimately. For substantially better sound, you should go and buy yourself an entirely new system. Buy a 6 channel deck, have 2 RCA's go to a 4 channel amp. Have the other 2 go to a mono channel subwoofer amp. Re-wire your new component speakers from the amp (since the signal that will be going to the speakers from your new amp will be coming from your trunk, re wiring is fairly easy because youre not working in the dash) Then wire up your subwoofers, and set your highpass/lowpass settings on the headunit. You will have an incredible sounding system, and for a lot less hassle than dealing with the factory mach system. But thats just me.