Since you have a line to line condition it is very easy. Mount your die (or your punch)
with screws and tighten. Let's say you have 3/8 dowel pins - use a 3/8 drill to spot the dowel holes from your die to the die set. Just spot and than use a drill 1/64 smaller to drill thru the die set. Use a .3748 dowel pin reamer and ream thru the die and the die set.
Line up you punch (or die) using the mounted die (or punch) as a guide. Make sure you use parallels to keep the components (punch) straight and bring down the top of the set. Clamp the heel of the punch to the die set, remove and transfer the screw holes. After tapping - mount the punch to the top (do not tighten the screws) and bring it down onto the die. Make sure the punch enters the die and tighten the screws. After you are satisfied with the fit - see if it will cut paper all around evenly- remove the top, spot the dowel holes with a 3/8 drill, drill thru with a drill 1/64 smaller and ream.