I just went through the exact same process on my '05 Ltd. with the 6-disc, 10 speaker JBL set up (actually, I used an '05 OEM head unit as the '06's seem unobtainable on the aftermarket) - a few issues that may come up:
(1) Your '06 may or may not have a JBL amp that supports the analog voice signals from the OEM Nav unit - the only way to know for sure is open up the panel in the right rear cargo compartment and check the part # of the amp - if it's an 86280-0W150, it does not support the Nav voice signals; if it's an 86280-0W340, it does - if it's some other number, your guess is as good as mine. Toyota seems to have randomly traded off amps in '05 and '06.
(2) If your stock amp does not support the voice commands, all is not lost - you can add a secondary amplified speaker for just the voice guidance - for example, the RadioShack 21-541A will do the trick and can be located under the seat or under the dash (a lot easier if you remove the speaker from its enclosure). NOTE: the Nav unit can not drive an external speaker w/o an amplifier.
(3) If you can get a Nav-ready JBL amp from a 4Runner (i.e. the above 340 part #) it will fit in your truck w/o modification, but you might loose operation of the two upper rear speakers making yours a 10 speaker system. You could trade out your amp w/ a JBL Nav-ready unit from another Toyota model (almost any JBL unit will work, but the sound won't be as good - the amps equalization are tailored to each model, e.g. Seqouia unit won't sound quite right in a 4Runner).
(4) Even if your amp is Nav-ready, you'll need to run a shielded twisted-pair from the head unit back to the amp and you'll need pin inserts for the 20-pin connector on the Nav and the 24 pin connector on the Amp - you can get the pins from Toyota, but they get about $20 each (you'll need 5) for them in the parts department - if you make friend w/ someone in the service department they may give them to you (they have a connector repair kit).
(5) You'll need to hook up the speed, reverse, and parking brake signals to the Nav and get one of the 5 pin connectors that mate w/ the Nav (the connector shell is about $11 from Toyota - the pins are best "gifted" from the service dept.)
(6) The Nav unit will fit in your dash, using the same brackets as the 6-disc unit, but you'll have some unsightly gaps around the edges since the factory OEM center dash trim piece is different for the Nav and 6-disc units. There's a post on this site about making yoru own filler for that gap, or if you're lucky, you can swap dash trim w/ someone that has an '03 to '05 4Runner that wants to upgrade from the single CD unit to the changer. If you're rich, you can buy the parts from Toyota - the dash trim piece is about $400 and you also need to swap out the A/C control assy at $800 (only the bezel needs to be changed on the A/C assy, but Toyota doesn't sell that part - only the whole assy with the circuit board, display, etc.).
Happy converting!
