Just a suggestion.....you might want to drop the driveshaft and check out the slip yoke and the internal bushing in the transmission tail housing. This bushing is often overlooked and if the slip yoke OD is galled, it will be noisy and this bushing will need to be pulled and replaced. This can be done with the transmission in place. It's critical to keep the T5 full of lube so that this bushing and the slip yoke splines stay lubed.
If the noise is definitely in the transmission and not the differential, it sounds like you're going to have to go for a box rebuild.
Hope this helps..
Dave