OP says diameter of the case just below the shoulder is 0.003 too big and the bolt won't close on some of his cartridges. He doesn't mention a headspace dimension. I'm guessing from what the OP has told us so far that (1) the bolt isn't closing due to too the case's headspace being too long, and (2) the case below the shoulder is .003" to big because the sizing die set too high. I think adjusting the sizing die as mehavey suggested in his #3 will solve both problems.
And I tend to agree that first, just get it to work, then fine tune it.