Have you got the expander ball set where the lower third lines up with the vent hole as stated in the instructions, or are you using it without the expander? I've gone around and around in my mind whether or not to use the expander, and since I don't take the time to turn necks, I decided I want the inside dimension (which most affects tension on the bullet) to be the most consistent, so I use the ball.
Runout on my two honed dies are .001-.0015", but I'm indicating off of the bearing surface of seated bullets just forward of the end of the case. Sounds like you're measuring the neck itself. What's the Runout of a loaded round, measured off the bearing surface of the bullet? That's a more meaningful number to me. And btw, .002-0025" ain't bad.