I'm not sure I understand.

So is the factory stereo like, integrated into the climate control panel? I'd say remove the factory stereo all together but maybe that isn't possible if it is somehow -part- of the dash. Anyway, I'd start by checking all my connections and making sure there aren't any exposed wires (even one's that might not be needed by the new pioneer deck) and no shorts. I just installed a DEH-3700 (not nearly as nice as a premier 9 series) but it was just a matter of removing the old factory unit and putting the pioneer deck in.