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yeah you can clock both sides, and is usually a good idea to do so that way the oil outlet is facing straight down, depending on the manifold you're using.
Just remember when you're clocking loosen the bolts a little and turn slow. There's a gasket (on t3's anyway) between the backing plate and the comp housing and you don't want to wreck it. The turbine side you don't have to worry about except make sure you torque the bolts in sequence so the turbine wheel sits level in the housing. Spin the comp wheel by hand afterward just to be sure nothing is rubbing.
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