Did you ever figure out the knocking/clicking at idle?

My 1999 4runner 3.4 115K started clicking about 3 months ago. It isn't constant, but will happen in PRN&D. It sounds like it is from the bottom of the engine. It will always quit if I depress the gas pedal, even if it only raises the rpm from 800 to 900. I have used full synthetic oil since 40K and high octane since 50K when I installed the supercharger.

I took it to my Toyota dealer and they said it was in the transmission bell housing (11 hours $1,055 in labor just to remove and inspect). Needless to say I refused and am looking for a different answer.