I had a 2003 Tacoma Xtra Cab TRD 4x4 with a 5 speed and that thing never let me down. I wish I still had it.
Unfortunately everything I have been reading points to the direction of failure. I have read some threads on tacomaworld.com about the problems on the 6 speed manual transmissions going back to the beginning of the Gen-2 Tacomas (2005+.) The FJ Cruisers share the transmission with the Tacomas, so you can find the same problems on those vehicles. Apparently the automatic transmissions on the Tacomas are also having some problems. You'd think with a problem that is already 5 years old there would be some sort of solution. Toyota has lost me as a repeat customer, that is for sure, unless I buy a truck that is pre 2005. And while I am on this rant, where is the manual transmission for the new 4Runners??
Worth a read;
Look around though, there are tons of threads with people experiencing all sorts of transmission problems. Oddly enough, most of those people are still very happy with their truck purchases. Toyota needs to get their shit straight or get shut down, too many problems with their vehicles recently.