I also noticed this noise when letting off the throttle on my facelift ep3. It's mostly noticable in 2nd 3rd or 4th gear.. I believe it does it in 5th and 6th also but it's hard to tell because of the other road noises.
I noticed that when i let the throttle off and press the clutch the noise disappears. But as soon as I depress the clutch the noise immediatley comes back. And also, when i press the clutch in and rev the engine a little there is no noise. As soon as i depress the clutch the noise comes back. So i believe the noise is not engine related.
I removed the header and mid shaft heat shields, so we can rule them out.
When in neutral and stationary, there is no noise other than the engine and normal engaged gearbox noises. So we can rule out the clutch release bearing. When i press the clutch in neutral, you can hear that the gearbox is disengaged and when you depress it you hear that it's engaged again, but no extraordinary rattles/grovles or anything that would imply a bad input shaft bearing or anything wrong.
The only thing that i didn't try is to put it in neutral while driving, to see if the noise will still be present or not
I did a bit of research in the past days and found that it happend/it happens to a lot of people. Some changed complete gearboxes, some replaced all the bearings in the gearbox but the noise persisted regardless.
Somebody, I think that on this forum, had the car at a honda dealership and even they didn't resolve the issue, and in the end they said to be a characteristic sound of the car LOL.
here is a video of the sound, it's not mine, but mine makes the exact sound:
https://www.youtube.com/watch?v=95rch-vj9cQ
i would be very thankful for any info regarding this noise.
update:
I've tried to put it in neutral when driving and when i rev it a little the noise is present.
Also i gave it another listen when stationary in neutral and with the hood open, it makes the noise but its not very noticable. Its definitely coming from the gearbox.
I would say that its the input shaft bearing on its way to fail.