I started setting my dies to "float" in the press, and at least for me, that has eliminated the vast majority of run out!
I just now went to my reloading room and pulled out 7 different loaded cartridges, from 3 different calibers, and got the following run out:
.0003
.00015
.00015
.0001
.0001
.0002
.00015
With those big 7/8-14 threads on the press AND dies, when you lock the die to the press, you will very seldom ever get things in perfect alignment, and about all you can do is hope for the best!
BUT! By allowing the die to "float" freely on the press, you have a much greater chance of holding the case in alignment during the sizing operation, and case necks are far less likely to be pulled off center on the upstroke.
Now, after having said all that, if your dies are cut off center or your press is worn out, or if your press ram is bent or otherwise not centered, then nothing short of replacing your press is going to help...