A possibly related issue is the true of the wheel. If it laterally out it will cause uneven rubbing on the pads. Make sure they are true.

Center pulls are great as they are really dual pivot brakes existing prior to the DP side pulls. When set up properly they are more than adequate. Keep in mind that back in the 60's and 70's, nearly all the top of the line models were Center pull, either Mafac "Racer" or Universal Mod 61, and for a good reason. The down side is the hardware required for the rounting. you need a specific cable stop for both the head tube and the seat cluster. Often used sets do not include these pieces, which can be frustrating. Here is an example of a Mod 61 from 1972 installed on a 1984 Trek 610