Before you consider replacing labor intensive items, you should contact the mechanic who replaced your clutch and flywheel, I can't imagine any decent mechanic doing a clutch job without replacing the throwout bearing (amongst other parts) while the tranny is down.
Usually, when a throwout bearing is going bad, it will make a whining noise when the clutch is depressed.
If this problem started right after the clutch job, you should take it back to the shop that did the work and see what they can do for you...at the very least, you'll probably get a diagnosis out of it.
2003 530i (Sport Package) Build Date: 02/03
Titanium Gray over Black
5-Speed Manual Transmission
Zeckhausen Modified CDV
Dinan Upgrades: High Flow Throttle Body, CAI, Stage 3 Software, and Free Flow Exhaust.
Horsepower: some is good, more is better, TOO MUCH is just right!
"If everything seems under control, you're just not going fast enough." ~ Mario Andretti
"What’s behind you doesn’t matter." ~ Enzo Ferrari