Since my minidisk player went out on my system, I've been looking at the upgrading my system as well.
I don't know anything about hooking up a changer to the factory deck. I'd imagine it would work, but you wouldn't be able to control the changer. I'd suggest getting a new deck, not only would it sound better, but it would look a little nicer too.
As far as the speakers and amp go, I have blown the front passengers speaker without ever turning the volume all the way up. The amp seems fine for pushing factory speakers but if you plan on adding more you might consider stepping up to something with more power. For the speakers I'm planning on replacing them with Infinity Kappa's which have a 3 year warranty (cost around $150).
Hope this helps some.
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'95 GT Convertable