If I punch the gas pedal hard from a standing position, such as at a stop sign, there's a clunk from what sounds like under the back of the car. I try not to hit the pedal hard, but occasionally it happens, depending on traffic conditions. Is this the start of a transmission problem?

 

Could be a center support bearing, which is the drive shaft center support, this makes a whining/ humming sound under the 2nd row seats when driving, it can make a clunk sound if its very bad or broken. If it breaks, it will slam the under side of the car. Also your noise could be motor mounts. also very common!

 

I have been having the same problem with my 98 ML. Took it to the dealer and was told the transfer case needs to be replaced. Quoted $7200, ouch! Such a shame 161000 miles on it runs like a champ but is now terminal.

 

Check the rear flex coupling, instead of a rear joint we have a rubber disc that connects the drive shaft tot he rear diff. Whn they get old abd cracked that can make a clunk as the shaft twists and makes contact with the diff.