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** I posted this in another thread but I think it applies to the OP.** The transmission is Aisin and it's a very close relative to the manual gearbox in the RWD 6MT used in the Lexus IS250. I drove a 2006 MT IS250 for two years, from brand new until 2008 (approx 35,000 miles). From my experience, I have heard VERY similar noises as described by the OP. I even had the infamous "jar of marbles" sound when shifting lower gears at slower speeds. I never had any mechanical problems with the IS MT clutch or tranny. I sold it to a work colleague and she and her husband drove it another 25k miles with no issues. I'm not saying you don't have an issue to be addressed, but I can say from my experiences the tranny and clutch did have a few quirky noises in my IS. BTW - I drove that IS hard and loved every minute of it.
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