2001 YZ426 Clunking from right side of motor

I recently purchase a 2001 YZ426 that did not run. Took it to Yamaha and asked them to go completely through it, ultimately they rebuilt carb, changed oil, adjusted valves, flushed radiator, serviced air filter, etc. I took it out and noticed a pretty significant clunking at idle and low RPM, goes away with some throttle, runs strong with massive torque, starts on 1 or 2 kick every time. Haven't owned a thumper before. Wanted to see if this is normal before I take it back to the shop.

You sure that is a 2001? Cause the 2000 model had a key holding the balancer gear in the right place.  If the crank gear nut gets loose, they start rattling around and the beat up their groove and get noisy.  They're pretty noisy anyhow, you know?  Maybe open it up and look. 

I am positive it's a 2001. Guess I will have them look at it. Just thinking they would not have turned it back to me if the clunking was something serious. They claimed to go through it thoroughly. I may be being overly cautious but the clanking sounds like a rod knocking in a car.

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