UPDATE: I just replaced the spark plugs and the two original coils. Problem NOT fixed
Still pretty much the same. After the car warms up and if I then let it sit and idle for a few minutes it cycles between running fine (700rpm) and then rough (drops to 550rpm). The rough cycle lasts about 5 seconds and then its fine for about 15 seconds. Repeats this way.
I did not see any burn marks on the wire boots and the spark plugs still looked very good - replaced anyway. I did not see any signs of ware on the old coils - replaced anyway.
I'm going to swap in one of the old coils for the #3 coil. The #3 was replaced 2 years ago. I don't suspect that will make a difference but its worth a try.
Its really difficult to listen to the fuel injectors especially the ones on the driver side under the intake. I put my ear in there and tried to concentrate on them. It did seem that the #6 injector was louder than the rest. Sounded like a washing machine instead of the clicking that is more usual.
My scanner is really only for emissions (IM) ready check and OBDII codes. It doesn't give any diagnostic info. I do have a fuel pressure gauge with a schrader port connector. Does the 4Runner have a schrader diag port? I could look into that and see if the pressure is dropping during the rough cycle.
diagnosis continues ...