Update: I had one of the motor mount replaced (CV6Z-6068-A) but the clunking noise is back. I went back to the dealer yesterday and now they say they can't start replacing all the engine mounts without knowing if it will fix the problem so I am back to square 1. I have been to the dealer about 10 times about this issue already so I am a bit frustrated. Here's how I can reproduce the problem; I am guessing if we share this info it would help.
1. It happens when the engine is either cold or hot.
2. I find a road with a very bad surface and a lot of short bumps. (Not hard to find with the crappy roads here in Canada LOL...)
3. I put the car in 1st or 2nd gear and do no exceed 30 KM/h. (I have a SE with the manual 5spd.)
4. Then I get a metal to metal clunking noise that is more than just annoying; I feel like my engine is hard mounted to the frame and that it's loose.
I really feel it's not a suspension issue. If you are still having this same issue; are you able to reproduce it at will or it just happen random?