'...he mic'ed the rotor thickness out and i was reading a .007 variation in thickness on one rotor and a .005 variation on the other.'
And normal. You should try simply cutting as perfect as you can ending with light opposed cuts to guarantee precision and then break down the setup and then reset it back up again after loosening the spindle and retightening the same rotor back down. You'll commonly find that the rotor which showed less than .002" runout seconds before now cannot be brought back in under .005" minimum regardless of orientation. The difference is the normal as supplied brand new clearance between the main shaft and the pilots used, to get them to slip on and off easily. The clearance then modifies multiplied through rotor OD and easily your new error. The piloting off the bearing bore has error in it as well, some places flat the rotor later and the bearing bores are done earlier in the manufacturing process. Goofy but I've seen it, the two are not the same cut setup. Even the rolled radius leading into it affects the flat even more. Radius is often not exactly concentric with the other cuts. Often you are set up on the radius (bearing bore END) rather then the true bearing bore, which is a gross mistake. Can't be done any closer than that, even if you try 50 times.
There are probably quality machines that can do closer than that but not the cheap ones found in most part stores now.
Why if you show a customer the variance you don't touch squat until he sees it, loosen the part up and you cannot get back there again. It throws the entire 'within .002"' TIR mantra out the window as totally unreliable except in lip service. I proved it out to store and district service managers when they started handing me loads of crap over it. Like I wasn't doing the job correctly, what a joke. The equipment was not good enough to do the job correctly.
Granted, runout and variation thickness are two different things. You can vary thickness by simply using a sharp cutter on one side and dull on the other. Two dull will do it too. Also, taking like .010" off one side and only .003" on other will make some screwy things happen. The heavier loaded cutter will deflect as vs. the lighter one. The heavy cut then vibrates to change the cut quality on that side, it varies more.
Some Chinese discs were so bad they were uncorrectable. And some of the work I saw come out of our shop, well, I was just shaking my head.