if the rotor is warped it is easy to check for runout, but it is better to find out why it warped in the first place, specially if they are new. i had a similar problem in our family van. had the rotors turned + new pads which was good for about 15k miles. when problem started up again i replaced rotors and pads then i noticed that one side was getting really hot to touch and discovered that a bad piston seal was causing sticking on one caliper. had to replace caliper but that was probably the original culprit in the first place...
1993 300e-2.8 - gone now <sigh>
"Do not adjust your mind, it's reality that's malfunctioning"