I couldn't attache the PDF but here's the text for that portion of the instructions.

REMOTE CONTROL FUNCTION SELECT
Follow this procedure to change the operating functions of remote controls already programmed into a system. You may change the remote control s default unlock operation mode so that pressing the UNLOCK button once causes all doors to unlock at the same time. Also, you may activate the AUX button function on 4 button remote controls.

1. Before you begin:
Open the driver s door and remove the key from the ignition switch.
2. Start the programming procedure. (Complete these steps within 40 seconds.)
a. Insert the key into, and remove it from the ignition switch 2 times.
b. Close, then open the driver s door 2 times.
c. Insert the key into, and remove it from the ignition switch 1 time.
d. Close, then open the driver s door 2 times.
e. Insert the key into, the ignition switch and leave it in.
f. Close the driver s door.
g. Turn the key from LOCK to ON 2 times (ending at LOCK).
h. Remove the key from the ignition switch.
i. The tail and marker lights flash 2 times, the buzzer chirps 2 times and the doors lock and unlock 2 times.*
*If the system does not activate the lights, buzzer and door locks 2 times, start over.


3. Select the operating functions for an existing remote control.
a. Press and release both the LOCK and UNLOCK buttons on one remote control at the same time.
b. Select one of the following modes:

Press and release the LOCK button to select double unlock function (press the UNLOCK
button twice to unlock all the doors.)

or

Press and release the UNLOCK button to select all door unlock function (press the UNLOCK
button once to unlock all the doors at the same time.)

or

Press and release the AUX button to select double unlock function (press the UNLOCK button twice to unlock all the doors) and activate the auxiliary output for the optional electric trunk release accessory.*

or

Press and release the PANIC button to select all door unlock function (press the UNLOCK button once to unlock all the doors at the same time) and activate the auxiliary output for the
optional electric trunk release accessory.*


c. The tail and marker lights flash 1 time, the
buzzer chirps 1 time, and the doors lock
and unlock 1 time.

Note: Repeat the above steps to select the operating functions for additional remote controls.

4. Complete the programming steps.
a. Open the driver s door

* Program for 4 button remote controls, only.
If the system activates the lights, buzzer and door locks 2 times, start over.

Does that process work on a 4th Gen with the stock keyless entry and immobilizer (no optional alarm)?

A dealer would never do all that, as they can change the setting in the body computer on a 4th Gen using their scan tool. This thread talks about such things that the dealer can change. If you buy a used 4Runner, the previous owner may have had the dealer make some of those changes.

Edit: Just answered my own question with a Google search. It sounds a lot like the process for the optional VIP RS3200 Toyota alarm system. See here:
http://www.customtacos.com/tech/file...rogramming.pdf

Yeah, not sure exactly how to post it here

I was beginning to suspect that. Oh well.

I am going to make the assumption that it works with alarms, and not just the factory keyless entry

Has anyone tried to get this to work on the factory keyless entry yet? It sounds as if the listed procedure is for the factory alarm only, not for the keyless entry system. Anyone? Bueller? Bueller?

Yes, that's what I was trying. Factory keyless entry only - doesn't appear to work. I guess you have to have the alarm to do it without the dealer.

Thanks for the pdf regarding the all door unlock setting. Do you happen to have the pdf to change the unlock time? Currently once you hit the "unlock" on your FOB you have 30 seconds before the doors relock. I'd like to change the timing on this. Like the 4 door unlock, the owner's manual says contact your dealer to make this change.

Please send me a copy!