U-joints, flex discs and CV joints are all problems that would produce the sound you're hearing. If it happens when you're doing something with the pedal, it's most definitely in the drivetrain system somewhere. You'll have to poke around, or have your mechanic poke around, and have a look. I'm not sure about the diff., but I always thought that they were pretty hardy. Good luck. I've never had to personally replace any of these parts, but lots of people here have, so they're very doable (I think).

Alex

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1983 300D (parked for four years)
2012 VW Sportwagen TDI Manual
2001 Miata SE
1962 Chevrolet Corvair Rampside