I have the mach 460 sound system in my 94 gt. I have been in Blueneonman's car before and as he mentioned: gutting the system is your best route for sound quality. His sounds a heck of a lot better than mine.
But if your just looking for a cd player to replace the stock cd player, any aftermarket is good. Anything is better than the stock crap they put in there because you'll be getting more wattage from an aftermarket one; although in theory, you shouldn't really need it considering Ford's setup of 460 watts going thoughout the system. But besides that, just get yourself a brand new head unit for now. Quality might jump up a little because of the wattage issue. Get one with atleast the power of 40w per channel. But keep in mind those speaker can't really hand much so you might have to tweak the bass/trebble settings.
Installation was cake for me. Do yourself a favor and get the connector from Best Buy or someplace ($20). It will save you the trouble of cutting wires and will probably be much neater.
It will come with two connectors: one for premium sound (mach 460) and one for just a regular setup if you didn't get the option. You'll also need a "amp integrator" harness. Should run you about $25.
You shouldn't need any other hardware except for 14-16 gauge splice connetors from anywhere (blue color).
Good luck.
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Green '94 GT conv. -- K&N filter charger, FMS 9mm wires, Accel hipo cap/rotor, 180* thermo, 14* timing, off road H-pipe in front of 2 chamber flow's, Steeda subframe connectors w/ crossbrace, and still workin' on the rest!
My 'Stang