90-120 days sound about right. There are a few members here who have waited that long for a special order. If your dealer is able to get it in a shorter amount of time, they're able to find your configuration that's already been allocated.
Here's the time line for mine. In early Nov. '05, my rep put in changes for my configuration on a Model 8668 (V6 Limited 4WD). In mid Dec. '05, I got word Toyota accepted the changes. My rep then checks his dealer's allocation every two weeks to find out when it would be arriving. On 2/6 my 4Runner is scheduled to arrive at port and awaiting to be sent to the dealer. I signed paperwork on 2/9, so that my truck is officially sold. I also got a card this week, from the service dept. thanking me for buying from the dealer and to visit them for service needs, with a brief survey.
My rep tells me that there's no special order for a Japan built Toyota, but only a special vehicle request. However, most customers are not willing to wait this long for a vehicle, and as long as I willing to wait, he didn't mind because it was a definate sale. I've bought from him before, he never tried talking me into accepting what's on the lot. I have asked about a V8 Limited 4WD in early Dec. because I was getting impatient on waiting. My rep's only fear was after the order got accepted, he may've missed the allocation that my configuration was on and another dealer or rep took it.
I bought a Tacoma last year which was also ordered. My understanding of the entire process between a US built and Japan built Toyota is, Japan built vehicles are preferenced to a certain configuration by the distributor, the dealer can only see what is being allocated, they cannot see the build schedule for the factory. So the dealer has to make changes to the configuration and wait for those changes to be accepted and then the changed configuration to be allocated to the dealer. In my area, all V6 Limited 4WD only come with side/curtain airbags, JBL 10-speaker sound system, moonroof, airbags and tow hitch. Only navi equipped 4Runners are V8 Limited 4WD. With a US built Toyota, the dealer can see both the build schedule and the allocation. They can also go in and make changes to the vehicle during the build schedule. For my Tacoma, my rep went in and added accessories, granted, I only wanted the TRD Off-Road package, running boards and SnugTop shell.
It's a long and agonizing wait, I almost gave up and gone for a V8 Limited for navi. The wait is worth it to get what you want.
Good luck!