Have you read through the RM.zip (don't know if a link is floating around somewhere anymore or not) or other Toyota Service manual for the 4Runner? Lot's of good information that you may have already tried.
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Auto Up Operation does not Fully Close Power Window (Jam Protection Function is Activated)

DESCRIPTION

If any door glass or a power window regulator motor does not operate smoothly, the jam protection function may be triggered automatically, resulting in the auto up function being unable to fully close the window.

HINT:

This symptom may occur for any of the windows.

INSPECTION PROCEDURE

HINT:

Since the power window control system has functions that use LIN communication, first confirm that there is no malfunction in the communication system by inspecting the LIN communication functions in accordance with the "How to Proceed with Troubleshooting" procedures. Then, conduct the following inspection procedure.

NOTICE:
When a power window regulator motor is reinstalled or replaced, the power window control system must be initialized.
After any door glass or a door glass run has been replaced, the jam protection function may operate unexpectedly when the auto up function is used. In such cases, the auto up function can be reinitialized by repeating the following operations at least 5 times:
Close the power window by fully pulling up the multiplex network master switch or power window regulator switch and holding it at the auto up position.
Open the power window by fully pushing down the multiplex network master switch or power window regulator switch.

PROCEDURE

1.

PERFORM INITIALIZATION (APPLICABLE LOCATION)

(a) Initialize the power window regulator motor (applicable location) WINDOW / GLASS: POWER WINDOW CONTROL SYSTEM: INITIALIZATION (2010 4Runner) .
NEXT

2.

CHECK POWER WINDOW CONTROL SYSTEM (AUTO UP/DOWN FUNCTION (APPLICABLE LOCATION))

(a) Check that all door power windows move when the auto up/down function of the multiplex network master switch and power window regulator switch (for rear LH and rear RH sides) is operated WINDOW / GLASS: POWER WINDOW CONTROL SYSTEM: OPERATION CHECK (2010 4Runner) .
OK:
Auto up/down function is normal (applicable location).
NG
CHECK WINDOW GLASS SLIDING MOVEMENT (APPLICABLE LOCATION)

OK
END (PROBLEM DUE TO INITIALIZATION FAILURE)
3.

CHECK WINDOW GLASS SLIDING MOVEMENT (APPLICABLE LOCATION)

(a) Remove the power window regulator motor.
(b) Install the window glass to the door glass run.
(c) Check if the power window regulator operates smoothly.
(d) Check that the window glass slides smoothly when sliding it up by hand.
OK:
Window glass slides smoothly.
HINT:

Make sure that the following conditions are met:

The window glass fits with the glass run without improper contact or deformation.
Foreign objects are not caught in the glass run.
CAUTION:
Perform initialization again.

NG
REPLACE POWER WINDOW REGULATOR MOTOR (APPLICABLE MOTOR)

OK
INSTALL WINDOW GLASS CORRECTLY (REMOVE FOREIGN OBJECTS CAUSING IMPROPER FIT OR REPLACE PARTS)
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