I'm nearby in Newport Beach. My 1999 RX 300 with 77K miles is getting a new (rebuilt) transmission right now at a the dealer where I bought it. I was able to get Lexus to assist with the cost because I'm an original owner and followed all of the maintenance schedules (all but one at the dealer). The information on this board and elsewhere helped me negotiate with Lexus.
Before I knew that Lexus would help, I checked the OC BBB found a transmission shop in Santa Ana with a rare AAA rating that would rebuild the transmission on a 2WD for $1,900 assuming that most of the parts are re-usable. If they have to replace all of the parts (unusual), the maximum cost would $2,800. It's called "Carlos Transmission."
Link: http://www.labbb.org/BBBWeb/Forms/Business...CompanyID=45283
Here's a list of other shops within 10 miles of my zip code: http://search.bbb.org/Results.aspx?z=92660...bb=0&rad=10
You've probably already had it repaired, but thought I'd post this in case it's still not addressed.