If your problem is not solved, I will tell you my experience. My T5 2007 1.9 5 speed also did the drive shaft.
Later I had a noise on overrun. Like a diff whine it would only happen on closed throttle and hard accelerating. I dropped the gearbox oil and it was very thin and grey from aluminium contamination. I had the gearbox pulled and we found the gearbox input shaft bearing had spun in the housing. The housing was ruined. This is apparently very common as the bearing is only retained by two thin circlips has no flange or step and is very thin. I had the housing machined and bushed and we have our fingers crossed. My mechanic has done several of these and the repair has been successful. He sees it as a serious design flaw and an inevitable failure for all 5 speeds at some point in higher miles.
Personally I would change the oil out regularly and as soon as any greying is evident or a SOS finds alloy I would have it pulled down before the bearing spins in the housing.
I am hoping the 6 speed in the T5.2 4motion is stronger? Anyone know?
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