dude, i am tryin to do the same thing. i have a kenwood dnx5120 and definitely DO NOT want to bypass my factory amp. its messy, expensive and is hard to retro-activate if that makes sense. what i mean is if u wanted to go back to your original system ( to sell the truck) it would be very very difficult. i have found a few sites that might help you, but if youve done any searching at all you have probably found them yourself already:
http://clublexus.com/forums/lx470-and-lx45...iring-help.html
following the posts and directions on this thread tells you how to use the factory amp via the pre-outs so you dont 'double amplify'. however its no easy feat and requires some plastic surgery and ingenuity. i am still in question about many things. also since the factory amp is turned on only by a factory reciever, when u install your new receiver, you must do something called jumpering, yes jumpering, the acc wire, so that the amp turns on when the car turns on. a lot of this wiring requires knowledge of what wire does what so for that here are a couple sites that diagram the lexus harness.
http://www.modifiedlife.com/1999-lexus-lx4...ring-schematic/
http://www.celiamania.com/wordpress/wp-con...lx470pinout.pdf
well thats about all i can help u with since i too am in the installation process and havent completed it yet. i cant even figure out how to get power to my damn kenwood from the truck. do i need to splice the power cable? ughhhhh