my first thought, failing turbo, no white smoke but sudden very rough shaking at idle, cruising and acceleration that can come and go. the noise and violent shake seem to come from the right side engine bay area. to me it sounds like the exhaust has fallen off right at the manifold(very loud and deep droaning). cel reads bad catalytic converter. where do i start this diagnosis???? could the cat be getting blocked off and stop the noise and shaking when its free. like i said it comes and goes but when its acting up there is a loss of power and very rough running coming from the right side of the car.

 

I believe you are having a misfire this just recently happened to my 03 1.8T check the ignition coils

 

ive experienced a bad coil before but this problem comes and goes. is that something a coil would do?

 

If your CEL flashes then you have a current misfire, if the CEL just stays on solid then most likely the cell block in the CAT has been damaged and may be causing an issue.. More details would help, or any other codes stored?