[FirstToy]

I had problems getting my door locks to re-program. I know it's a different model (03 4Runner) but maybe it will help you figure yours out.

This is from another 4R owner:
I wanted to choose option (B):
All the side doors and back door are automatically unlocked when the automatic transmission selector in moved to the "P" position with the ingnition switch in the "ON" position.

The Manual says:

1.) close all the side doors and back door
2.) Turn the ignition switch to the "ON" position
3.)within 3 seconds after the switch is turned to the "ON" positon; pucsh and hold the rear of the power door lock switch for 5 seconds with the automatic transmission selector in the "P" position.

I did this several times with no success.

Then I read the manual again...

On the same page in a later paragraph it said;
All the side doors and back door automatically lock and unlock when you release the power door lock switch. This indicates the function is set. If all the side doors and back door do not loack and unlock, the time the switch was held may be too long or too short. Perform the procedure over again.

Anyway, I tried it again (being more careful to hold it down for the prescribed 5 seconds) and it worked.