I've taken bits and pieces from other user postings on this topic and made my new remotes work with this procedure. Thanks to all those that contributed partial instructions.

How to program a remote control for a 2000 4Runner

Step 1 - open drivers side door and get in your vehicle.

Step 2 - put key completely into ignition,then pull out.

Step 3- with door open, lock and unlock 5 times on door console (ten clicks total).

Step 4 - close door then open door.

Step 5 - lock and unlock 5 times on door console (ten clicks total).

Step 6 - put key completely into ignition then turn to the on position then pull key out (you will now hear the door locks lock then unlock a couple of times)

Step 7 - now quickly press the lock and unlock buttons at the same time only for about a second.

Step 8 - then quickly press the lock button for just a second.

- If locks cycle once, programming is sucessful, exit car and close door.

- If locks cycle twice, the programming didn’t work; retry steps 7 & 8 immediately. If locks cycle once, programming is sucessful, exit car and close door.

Try remote. If it doesn’t work, start all over. This procedure works for sure.

Thanks,
This really works but just a note to avoid confusion.

In step #7 and #8 the buttons referred to are on the remote itself.

Saved me 60Bucks.