"Houston, we have a problem"

[Rapidrob]

Thank you for all you photo's and measurements. you nailed it. Your sizing die is the culprit. Just because dies are new and expensive, that does not make them perfect. Many times over the years I've had to send dies back. The reamer used to cut the die was: Too worn,too small,chattered,off center,etc.
your on the right track with honing out the neck. My general rule of thumb is to never move the shoulder back once it has been fired out of my rifle. My dies are made to small base size and neck size only. It seems to work well in my semi-auto rifles.