My 2001 Dodge Ram 5.9 V8 still misfires but not enough to trigger the sensor for the Check Engine Light?

I got a Check Engine Light code for a misfire on cylinder #1. After getting new spark plugs and spark plug wires the code went off. I took it back to a shop to double check if the misfire was gone they did a test for 2minutes and they said a have small misfires on multipul cylinders, but the misfires arent often enough to set off the CEL. What can I do to fix all the misfires?