I have already shortened the shell holder from other uses, I guess I could shorten it some more, but at this point I think the body die is going to get shortened.

If you are not lubing the case neck ID, your neck expander will pull the case shoulder forward giving you the conditions you described. You may want to check this out.
The Redding Competition dies don't have an expander, oddly enough I don't think you can even put an expander on the neck size die at all.

I have a body die and a neck size die, and of course a seater die.

Body die is fairly cheap, maybe I will call Redding and see if they will send me a new one that has already been shortened.

The Redding body die is a very simple die, just bumps the shoulder and case walls, doesn't touch the neck at all.