Anyone know if it is a characteristic of an '06 to make a clunking noise (not super loud, but noticeable) while shifting from 1st to 2nd at around 4500rpm? My car only has 35,500 miles and a brand new clutch including flywheel. I am hoping it isn't something serious.

 

Do you know if the previous owner installed a short shift extension in the shift box? That mod makes a very distinctive clunk noise. An easy way to check is to measure the throw of a another mini and compare it to your throw length. If yours is significantly shorter and a little harder to shift then you probably have that mod. However, I really enjoy the mechanical feel it provides, and if you have a performance clutch and single flywheel it makes shifting much more natural to match with the narrower friction zone.

 

Check your motor mount...
Bet it has failed....and the motor is thrashing about...
The motor mount is basicly a rubber ball on filled with oil, with a bolt sticking out, in a metal can...with time, the rubber fatigues, and tears. The oil leaks out, and the motor moves under high stress, "thumping" as it bumps back and forth....
A mount is about $180-200 installed at an independent shop, or $100 in your driveway....

 

I should have put in my original post that the motor mounts were replaced. 😔