Cobra,
In 06', The JBL Synthesis sound system is an option in the Sport and Limited models. Most Limited models will come with it and most Sport's will not.
My brother is in upper managment at Toyota here in Wichita, KS and he was able to help me when I put my order in for my 4Runner. I wanted two options that Sport Editions almost never come with in 06' and that was the JBL Synthesis 6 Disc sound system and Homelink. He was able to get on the computer and check the whole country to see where I would be able to drive to get me a 06' Sport with those two additional options and there was only one or two out in southern california but wasn't the color I was wanting. One was red and I can't remember the other.
When we talked to the Toyota Rep assigned to this part of the United States, who is also a friend, he told us that in 05', the JBL Synthesis system was easy to come by but in 06' it's almost always a custom order. Again, that is referring to a Sports Edition.
So all I know for a fact is that back in January of this year when I ordered mine, there were only 2 - 06' Sport Edition 4Runner 4x4's with the JBL Synthesis 6 Disc sound system anywhere in the United States, that was still new. Lot's of them had the homelink but I was willing to sacrafice that option so that I wouldn't have to wait a few months to get one with JBL. However, that didn't work out so I ended up waiting until early April to get mine delivered here.
I happened to read this last last night and asked him if it were possible to even custom order a 06' 4Runner of any model with the JBL Synthesis sound system with only one disc and he said no. It's because Toyota only makes two head units for the Synthesis sound system, one of which is an in-dash unit that holds 6 discs and the other being a navigational unit that only holds 4 discs.
Also, a couple other important pieces of information, there were no changes made to the 07' 4Runner in any of the models and you might ask whatever dealer you are dealing with to print you off what is called a Vehicle Inquiry Report on whatever 4Runner you are looking at. The Vehicle Inquiry Report is like a cheat sheet or a more detailed window sticker of each vehicle. It lists not only the individual options and prices, but also the invoice prices that the dealer had to pay for each option and the vehicle as a whole. The Vehicle Inquiry Report listed the 6 disc CD player with the standard head unit as the premium sound system, just as a Tacoma would read. They call it the premium sound system because it has the 6 discs instead of the standard one disc head unit. The sound is actually all the same. But I think you have to pay an extra $200 for it or something.
Anyway, I'm glad I waited to get an 06' Sport with JBL because I think it sounds great. The reason I like it so much isn't because of how clear it sounds at high volumes, but because of the fact that it comes with a splitter that actually breaks up each song into 10 channels and spits it back out through the speakers at slightly different volumes for each speaker to give you a surround sound type enviroment. The amplifier and subwoofer are nice too but anybody could throw in those two options easily and make it sound good if they were willing to spend the money.
My recomendation would be to go back down to Toyota and jump in a Limited, which will most likely have the JBL Synthesis, and play with it. Take a couple of CD's that you like and just see what you think. After doing that for awhile, cycle through the tuning options and turn off the surround sound to hear what it would nearly sound like in a standard 4 Runner. Because believe me, there is a HUGE difference.