I fitted an aftermarket stereo in my mk1 and mk2 GS300's. Much better than the standard setup for sound.
The changer is in the boot, on the right hand side, if it had been removed, it would stick out like a turd on a bowling green, as the boot floor liner is moulded around it. The amp is located underneath the changer. If you are not bothered about returning it back to standard later, then just cut the wiring at either end (headunit and amp - to effectively bypass the amp). By bypassing the amp, you don't need to run new speaker cables in. Obviously with the amp bypassed, the sub in the rear shelf doesn't work. I fitted a Vibe active sub in the boot and removed the factory sub.
If you need any specifics, let me know.
p.s. None of the fascia adaptors I could find advertised for the mk1 would actually fit (they were all for left hand drive cars and the opening isn't symmetrical). I bought the one from Toyota for the Aristo. There are details (part numbers) for the fascia in the link in my signature "Mk1 Single Din install", hope it helps.