I am getting a whine in my WC T5 seems to be more pronounced in 4 or 5th gear. Also over 40 mph. It goes away when I press the clutch down. Fluid is new and full and never went low. About 2k miles ago the trans was rebuilt and clutch and associated items were changed. I just tried to change the throw out bearing it did not help. I pulled the T5 cover while in there and saw nothing obvious.

So what do you bet on? Input shaft bearings?

 

Bump. Having similar issues, and driving yesterday, the car made a violent rumble, then smoothed out. This was the only time I didn't disengage the transmission when the rumble started to happen. Thought the car may have fixed itself but the transmission seems to still be having issues.

 

Here is what I know so far. I took out the trans during the winter and found a rough throwout bearing. I replaced that along with the fork and pivot ball. I took the cover and tail shaft off the transmission and saw nothing out of place. Took it out again and found the noise was still there mostly in 3,4,5th. I am confident it is a bearing in the trans now and most likely something on the back half. Soon I will swap it with one of my old units and check this one. If it is just a bearing I will probably upgrade the case and 5th gear support and reassemble.

 

Just an update turned out to be a broken pinion tooth in the rear end. The torque arm was transmitting the rear noise perfectly to the trans area messing with my ears.