I recently purchased an '06 evo and have noticed this noise since. I put new fluids into the transaxle, TC and rear diff shortly after buying the car and the noise persists regardless of oil change. I've taken note of how to reproduce the problem so maybe someone could help me figure it out. In the morning after it's been sitting overnight it'll make a clear rotational knocking noise for a short moment when beginning to accelerate around 1-2k RPM but the noise also sometimes occurs during cruising in any gear, again around the 2k RPM area although not as pronounced as that first initial start. Another way to produce the noise is cruising over rough bumps, again the knocking noise occurs as if somethings bouncing around inside one of the drivetrain housings. And just recently after having made a modest push through gears 1-4 and later reaching my destination, on the next start up it was knocking loudly in neutral and at idle. When I started driving again it settled and went away or rather occured the same way as stated above. Now this leads me to wonder what part of the drivetrain is at fault? I'm thinking possibly the front diff or transfer case but I'd like other opinions. Thanks in advance.

 

Sounds like the Clutch. Is it the original clutch and how many miles on the 06?

 

It is the original clutch with only 18k miles on the car. I did however buy the car used at around 16k so I don't know how the previous owner treated it. Engagement point is still high, my understanding is that as it wears itll start engaging closer and closer to the floor. Also I haven't experienced any clutch slippage for what it's worth. Oh and I'd like to add that there's no feedback from the pedals which would point to a damaged clutch component. I don't believe the clutch could be intermittently causing a noise. I guess what I'd really be interested in is whether any Evo owner has experienced similar symptoms, my searches only brought up concerns over worn throw out bearings or input shaft bearings.

 

Just had the thread moved into this section to hopefully get more feedback.

 

I know this is an old thread, but I just wanted to share some insight. I experienced the same thing and would hear some knocking inside the tranny. It was specially noticeable while idling and have the AC the on. And when the AC would kick in and when the car is under load, I'd hear the sound. It reminds me somewhat of like marbles in a pocket. I just had the clutch replaced on my car and it was the release bearing. I played around with it and noticed that it had a lot of play and was wiggly and at the same time was dry as heck. Don't know if this might be your problem, but you can certainly have it checked out.