The factory radio isn't tied into the security sysem in that vehicle. Who told you that? Thats only on 96-98 civics. If you were to do that, you'd be relocating it somewhere else in the vehicle, like under the seat for instance. You can alway try it, but the correct harness used to do that is rather expensive and i'm 99% sure it wouldn't even work with your vehicle. Different plugs. I don't think it's related, we(Best Buy) just put a Pioneer double-din navagation system in a 99 V6 that had factory security without any problems. It was just a pain finding the reverse wire.