Does the noise happen when you are deaccelerating while still in gear?
Does it sound like a sort of grinding sound?
I just got my clutch replaced and this sound still persists. I think it's the Intake.
Sounds like grinding metal when you engine brake, and pressing in the clutch or giving it gas makes it go away.
I doubt that it's your TO bearing, cause mine got replaced with the clutch, and it still makes this noise.
I had the same noice while engine braking, grinding noise stoped after a pressed the clutch. I told the dealer that there was an annoying grinding noice, they test drove it and they fixed it under warranty. I don't have the receipt that shows what they did cause I lost it. But this happened about 1 year ago. It now seems like its coming back.