I Found the programing for what is supposed to work for a 03-05 4Runner and it works on an 06. Keep trying...it will work. Keep your money in your pocket and out of the $tealer's.
1. Drivers door open, key removed from ignition switch
2. Within 5 sec insert and remove key from ignition switch twice
3. Within 40 sec close and open driver's door twice
4. Insert and remove key from ignition switch
5. Within 40 sec close and open driver's door twice
6. Insert key into ignition switch and close driver's door
7. Switch ignition ON and OFF once to program a remote transmitter while retaining the original codes. Switch ignition ON and OFF twice to program remote transmitters while erasing the original code. (Three times to check how many remotes are currently registered)
8. Remove key from ignition switch
9. System should now lock and unlock vehicle. Once, twice or five times depending on which mode has been selected. One to four times, slowly, to indicate how many remotes are registered
10. Within 40 sec press and hold remote transmitter's LOCK and UNLOCK buttons together for 1.5 sec and release.
11. Within 3 sec press remote lock button
12. System should now LOCK and UNLOCK vehicle. Once to confirm registration, twice to indicate programming has failed
13. Within 40 sec repeat steps 10-12 to program additional remote transmitters. Up to 4 remote transmitters can be programmed.
14. To exit programming mode open the driver's door
Note: pay careful attention to the timing of the intervals especially in steps 10 and 11. Holding the buttons too long or too short will cause the programming to fail. Multiple attempts might be necessary.