I have a H22A4 mated to a M2B4 JDM Lsd transmission (in a EG hatch).

Engine was rebuilt, and transmission torn apart to replace 5th gear syncro. After about 1500 miles, the powertrain developed a weird growl (almost sounds exactly like a bad power-steering pump, although mine is deleted..). The growl goes away 100% when the clutch pedal is pressed in, unless the vehicle is rolling. Anytime the clutch is engaged, it'll growls with the rpm regardless of gear, or neutral.

Every forum post showed bad input shaft bearing to be the culprit. I tore the transmission down again, replaced the ISB with an OEM unit, got a new OEM throw out bearing (just in case), new clutch kit, resurfaced lightweight flywheel, and absolutely nothing changed at all. Noise is still there.

The noise is definitely coming from the flywheel area, but its very hard to pin point where at exactly.

I cant figure out what it is, so any input/ suggestions would be appreciated.

Key notes;
Growls/ whines like a bad power-steering pump when clutch pedal is NOT pressed in, or if vehicle is rolling. Power steering is deleted on manual rack, so not PS related.
Noise goes away 100% if car is stationary, and clutch pedal is pressed.
I noticed a vibration at 80mph+ about the same times the trans noise appeared
Very slight vibration can be felt in the car when the growl is present and car is stationary. Press clutch pedal in, and idle slightly smooths out.
New OEM input shaft bearing, and throw-out bearing solved nothing.
No noticable damage inside trans case when torn apart. Even ISB looked good.

 

Sounds like differential bearings to me.

 

From the research I did, differential bearings being worn would only make noise (growl/ whine) when the wheels are moving, correct? It makes the growling/ whine noise even when stationary.

 

Must have missed that when I initially read your post. That is interesting. Any shavings in the trans fluid or engine oil? What kind of condition is the engine in?

 

Fluid came out clean, but I also didnt inspect it very closely. I drove the car one last time with this trans to note the symptoms a bit closer, and after driving it a bit, I noticed the diff bearings are bad as well, as I heard a strange whine while driving that went with wheel speed, but the other whine that comes/ goes with the throw-out bearing being depressed is still there. Pretty much assuming trans is needing a full rebuild at this point.

I ended up replacing the transmission with another M2S4 trans I found at the local junkyard, and all the noise went away, so its definitely something in the trans thats bad.