When hearing a clunk... and (for example), knowing it's drive-train related... is it always something like a a mount, or flex disc...?

What I mean is: When hearing a clunk upon downshifting (only will happen when downshifting into 2nd gear at low speeds.. apprx 25 mph), could it be something within the trans?

Reiterated... Is it possible/common/whatever that a clunk is occurring internally within the transmission?

(Still feel the 'acceleration resistance' and have a clunk even after replacing flex disk.... it was perfect for a few days after replacement... maybe it neets to be retightened!?)

__________________
2006 E350 w/ 155k miles (Daily Driver)

Previous:
1993 300E 3.2L Sedan w/ close to about 300k miles
2003 E500 Brilliant Silver (Had 217k miles when totalled!)
1989 300E with 289,000 miles (had for <1 yr while in HI)
03 CLK 500 cabrio (Mom's)
2006 C230k (Dad's)
1999 S420 (Mom's/Dad's)
2000 C230k Sport sedans
2001 CLK320 Cabrio (Mom's)
1995 C280 My First Mercedes-Benz... (155k miles. EXCEPTIONAL AUTOMOBILE. Was Very hard to let go of!)