i have a lincoln ls is it possible to hook up the stock 6 cd changer to the avic d3??

It *might* be possible if your stock radio is a pioneer.

I have a Lexus LS400 and the stock radio is a pioneer, there is someone on the Lexus forums who changes something in the circuit board to match the Pioneer head units so that it works.

No it's not. The stock changer ain't gonna work.