random misfires have nothing to do with lift. a 600 lift stock cam would run without the code setting.
It doesnt "screw" with it, it just eliminates misfire detection. Sometimes it may eliminate knock detection.If P0300 sets on you, it'll limit things and screw with how it runs.
There is no breakin required, your motor is only going to last a few hundered miles anyway, so i wouldnt waste the time getting it "tuned".