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Join Date: Jul 2015
Location: West Linn, Oregon
Posts: 99
Bikes: Cannondale R1000, Redline Disc R, 1982 Colnage Superissimo, Specialized M2 Stumpjumper, Trek Elance, 1984 Trek 610
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Hard to diagnose without hearing it,but here are some questions to try to narrow it down:
Is the clicking coming from both wheels or just one?
Is it cyclic with the rotation of the wheels, I.e. does it happen at the same point in the wheels rotation?
Have you checked The clearance between the rim and brake pads?
Are the new wheels true? Do they wobble or hop?
Does it happen when you're pedaling and when you're coasting.
The fact that it decreases as you turn indicates wleel flex is playing some part in the process. You might take the whole bike to another shop for a scond opinion.
Good luck.