alhade,
You don't tell us whether the nav system you're buying is an afterrmarket unit, or the Lexus factory one. There is a big difference, and you are chewing off a lot of work.
The factory unit has a backup camera, the wiring for it goes from the rear to the dash (read a lot of interior panels have to come off, as well as carpeting). Then there's the GPS unit's antenna and its wiring from the dash to the overhead mirror area, and again a whole pile of panels have to come off.
Do the necessary wiring harnesses for the nav unit already exist in the car, or do you have to pay through the nose for them from Lexus? Do you have the wiring diagrams? The center console surround for the nav unit is different from the standard non nav console surround. Can you get one? Does the nav unit come with the latest update dvd, or do you have to buy it from Lexus, read $$?
And the biggie ... are you going to do the work .... or are you going to pay someone whose done it before? It isn't as easy as just changing out the radio. At the time that the car was built its an easy job. Not so in this case. Like I said ... you are chewing off a big chunk and may be in for a lot of frustration and far more expense than would make the addition of a nav system worth it.
Personally, the only way I'd tackle the job is if I already had the wrecked car with the nav system already in it, and another daily driver to use while I tackled the job of the change over.