after living with the dreadful clunk for a bout 5 mos now when I disengage the clutch (not all the time, it's intermittent) and some researching on line (mostly here), I finally took it to the dealer for their expert diagnosis. Also, i've recently developed a knocking noise on top of the engine (cam and vanos area) but that's another topic ( $450 just to open up the valve cover and check cams and vanos)...
anyway, they told me that the clunk is due to the transfer case actuator needing replacement, about $1500 for parts and labor plus new fluid. so , i think i will try to change the fluid first to see if that makes a difference .
2004 6MT w/93K miles