Getting older ain't for sissies. My best success for die alignment has always come from setting each die up individually, and using the shell holder on the ram, along with a small steel plate to square the die to the top of the shell holder. That doesn't help much with lateral die alignment, and I hate relying on slop in the shell holder to allow the case to "float" to the die center. Then the expander/decapping stem needs to be aligned to the case mouth as possible. Usually, the best you can do is get the stem tolerably straight. For bottleneck cases, the neck expander is usually the common culprit for neck runout. As far as that goes, the expander is a major culprit for crooked seating in straightwall cases as well. We've had a couple of discussions about M Dies and Dillon powder funnel shortcomings.
Since we already have a thread started, it's be a shame if we didn't wring this topic out a bit.