A throwout bearing is pretty far away from the intake. I can't even picture what your friend is trying to suggest. Try putting your car up on jackstands and start it. Look around for things that could rattle. Maybe use a mechanics stethescope to see if you can pinpoint the sound.
Have you adjusted your clutch recently? Maybe a little too loose so that the release fork is rattling?
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351W 89 Mustang GT Convertible