1. Take the new key and one master key that can start your 4runner(old key) into the 4runner with you and close the driver's door.(immobilizer light should be blinking)
2. Insert old key, remove old key, Insert old key, remove old key,
Insert old key, remove old key, Insert old key, remove old key,
Insert old key (immobilizer light should be off from the first insertion)
3. open and close driver's door six times (immobilizer light should be off)
Step 2 and 3 need to be done in less than 35 seconds(pdf says 35 seconds)
4.remove the old key. (immobilizer light should come on(steady on, not blinking))
5. insert the new key(immobilizer light should be blinking)
Then just sit there and wait, after about one minute the blinking immobilizer light should go off and you're done.
Whole process need to be repeated for any additional keys, the just programmed key could be used as the "old key" for the additional keys.
If there are 5 master keys registered with the immobilizer, it won't accept any more(and I don't know how would it tell you this, so just do a erase if you can't get it to work after trying for a few times). You have to erase them using a similar method(bring in just an old key, insert+remove one more time and open+close one more time, after the 7th close of the driver's door the immobilizer light will stay lighted for one second, remove the old key quickly after that and all but that one you just removed are erased.)