I've fitted the hub/bearings and disc to one side now. Checked the runout and it's 0.004", twice as such as it should be. Maybe I've got some crap between the drive flange and disc but I thought I'd cleaned it up alright. The manual says to try repositioning the disc on the drive flange but should this be necessary with new parts?
How does it compare to the drive flange?
Good question, I'll check that next time.
Guessing they are the S type. Often people do not get the drive flanges seated fully. So you can also compare the edge of the disc flange that is just outside of the drive flange. They should have the same runout.