The shim punches I have used are about 3 x 3.5, but could be what ever you want. The punches are on size, and the die holes are +0.002. The die plate should be 0.375 O-1 or W-1 tool steel, and should be ground after heat treat.The top plate is normally 0.375 0r 0.500 poly carbonate, but could be steel if you don't need to see the work, and the holes are +0.0005 for a tight slip fit on the punch. The punch OD is relieved about about 0.5 from the working end, so the punch slips out easy after punching. Normal gap between the top and die plate is around 0.125.
Hope this helps