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I would question putting two different calipers on the rotors. One might take more psi to push the plungers out then the other. Could be the reason for pulling to one side.
I agree 100% if you are doing it do both at the same time and make sure you have the same calipers. I would think there could be a slight difference in the different brand of callipers causing your problem if your tires are aired properly. Just my .02