On a few occasions I have heard some odd "clunking" sounds. It seemed to happen most often when making a left turn. The best description I can provide is it sounds kind of like a refrigerator ice maker when it is dropping ice into the ice bucket. I happen to come across someone's build thread where they said the dealer noticed their rear remote reservoir did not have adequate clearance from the body in the wheel well.
Sure enough, I got under the 4 Runner today and my driver side remote resi was actually touching the body! I got out my dremel and cutting wheel and took care of that. I haven't done the passenger side yet but I will post my findings regarding any remaining clunking sounds...
UPDATE: CLUNKING SOUND GONE!
BEFORE:
AFTER: