I had this clunking that altered with speed, not RPms, and it turned out to be my rear differential, (on a GMC, not Honda) anyway, the differential made that noise, and after a while the ring and pinion just broke and the car would not go over 5mph. Since the Element is not RWD (to my knowledge) I don't think that's the problem, but I assume there's a similar differential up front to change the spin direction to the wheels. Maybe the problem lies there, or in the transfer case. I don't see why the transmission would cause it...