Imperium11

I just purcased a 1992 LS400 with the nakamichi system in it
my plan is to install my Alpine IVA-w203
alpine amp and alpine sub while leaving the rest of the speakers alone, what is the best way of doing this
There is a harness made for the models with an amp but 93+ will this work for me?
I read that using the harness for non factory amped models that you haveto run all new speaker wires. Is this true i would really like to know?
Or will it only cause me to lose the function of the factory sub
also if it makes any difference the factory cd changer does not seem to work

please help